Source: nipype Version: 0.4.1-1 Severity: serious Justification: fails to build from source
nipype FTBFS in unstable: | python ../tools/ex2rst \ | --project Nipype \ | --outdir /build/nipype-rFhixh/nipype-0.4.1/doc/users/examples \ | ../examples/freesurfer_tutorial.py \ | ../examples/fsl_tutorial2.py \ | ../examples/fsl_feeds_tutorial.py \ | ../examples/spm_tutorial.py \ | ../examples/spm_face_tutorial.py \ | ../examples/spm_auditory_tutorial.py \ | ../examples/fsl_dti_tutorial.py \ | ../examples/camino_dti_tutorial.py \ | ../examples/connectivity_tutorial.py \ | ../examples/dtk_dti_tutorial.py \ | ../examples/dtk_odf_tutorial.py \ | ../examples/spm_tutorial2.py \ | ../examples/spm_dartel_tutorial.py \ | ../examples/dartmouth_workshop_2010.py \ | ../examples/nipy_tutorial.py | examples2rst finished. | rm -rf api/generated | #python ../tools/build_modref_templates.py | rm -rf interfaces/generated | python ../tools/build_interface_docs.py | /usr/lib/pymodules/python2.6/matplotlib/__init__.py:890: UserWarning: This call to matplotlib.use() has no effect | because the the backend has already been chosen; | matplotlib.use() must be called *before* pylab, matplotlib.pyplot, | or matplotlib.backends is imported for the first time. | | if warn: warnings.warn(_use_error_msg) | WARNING: Empty - nipype | WARNING: Empty - nipype.algorithms | CreateNifti | Generating inputs/outputs doc for: nipype.algorithms.misc CreateNifti | Distance | Generating inputs/outputs doc for: nipype.algorithms.misc Distance | ModifyAffine | Generating inputs/outputs doc for: nipype.algorithms.misc ModifyAffine | Overlap | Generating inputs/outputs doc for: nipype.algorithms.misc Overlap | PickAtlas | Generating inputs/outputs doc for: nipype.algorithms.misc PickAtlas | SimpleThreshold | Generating inputs/outputs doc for: nipype.algorithms.misc SimpleThreshold | TSNR | Generating inputs/outputs doc for: nipype.algorithms.misc TSNR | >>> DEBIAN doc building with missing externals >>>: gcd() takes exactly 2 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: gen_info() takes exactly 1 argument (0 given) | >>> DEBIAN doc building with missing externals >>>: orth() takes exactly 2 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: scale_timings() takes exactly 4 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: spm_hrf() takes at least 1 argument (0 given) | SpecifyModel | Generating inputs/outputs doc for: nipype.algorithms.modelgen SpecifyModel | SpecifySPMModel | Generating inputs/outputs doc for: nipype.algorithms.modelgen SpecifySPMModel | SpecifySparseModel | Generating inputs/outputs doc for: nipype.algorithms.modelgen SpecifySparseModel | SpecifySparseSPMModel | 'SpecifySparseSPMModel' | ArtifactDetect | Generating inputs/outputs doc for: nipype.algorithms.rapidart ArtifactDetect | StimulusCorrelation | Generating inputs/outputs doc for: nipype.algorithms.rapidart StimulusCorrelation | WARNING: Empty - nipype.interfaces | WARNING: Empty - nipype.interfaces.afni | WARNING: Empty - nipype.interfaces.afni.base | WARNING: Empty - nipype.interfaces.afni.preprocess | camino setup test | camino teardown test | WARNING: Empty - nipype.interfaces.camino | Conmap | Generating inputs/outputs doc for: nipype.interfaces.camino.connectivity Conmap | AnalyzeHeader | Generating inputs/outputs doc for: nipype.interfaces.camino.convert AnalyzeHeader | DT2NIfTI | Generating inputs/outputs doc for: nipype.interfaces.camino.convert DT2NIfTI | Image2Voxel | Generating inputs/outputs doc for: nipype.interfaces.camino.convert Image2Voxel | NIfTIDT2Camino | Generating inputs/outputs doc for: nipype.interfaces.camino.convert NIfTIDT2Camino | ProcStreamlines | Generating inputs/outputs doc for: nipype.interfaces.camino.convert ProcStreamlines | TractShredder | Generating inputs/outputs doc for: nipype.interfaces.camino.convert TractShredder | VtkStreamlines | Generating inputs/outputs doc for: nipype.interfaces.camino.convert VtkStreamlines | ComputeEigensystem | Generating inputs/outputs doc for: nipype.interfaces.camino.dti ComputeEigensystem | ComputeFractionalAnisotropy | Generating inputs/outputs doc for: nipype.interfaces.camino.dti ComputeFractionalAnisotropy | ComputeMeanDiffusivity | Generating inputs/outputs doc for: nipype.interfaces.camino.dti ComputeMeanDiffusivity | ComputeTensorTrace | Generating inputs/outputs doc for: nipype.interfaces.camino.dti ComputeTensorTrace | DTIFit | Generating inputs/outputs doc for: nipype.interfaces.camino.dti DTIFit | DTLUTGen | Generating inputs/outputs doc for: nipype.interfaces.camino.dti DTLUTGen | ModelFit | Generating inputs/outputs doc for: nipype.interfaces.camino.dti ModelFit | PicoPDFs | Generating inputs/outputs doc for: nipype.interfaces.camino.dti PicoPDFs | Track | Generating inputs/outputs doc for: nipype.interfaces.camino.dti Track | TrackBallStick | Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackBallStick | TrackBayesDirac | Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackBayesDirac | TrackBootstrap | Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackBootstrap | TrackDT | Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackDT | TrackPICo | Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackPICo | camino2trackvis setup test | camino2trackvis teardown test | WARNING: Empty - nipype.interfaces.camino2trackvis | Camino2Trackvis | Generating inputs/outputs doc for: nipype.interfaces.camino2trackvis.convert Camino2Trackvis | Trackvis2Camino | Generating inputs/outputs doc for: nipype.interfaces.camino2trackvis.convert Trackvis2Camino | WARNING: Empty - nipype.interfaces.cmtk | >>> DEBIAN doc building with missing externals >>>: cmat() takes exactly 7 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: create_endpoints_array() takes exactly 2 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: length() takes at least 1 argument (0 given) | >>> DEBIAN doc building with missing externals >>>: save_fibers() takes exactly 4 arguments (0 given) | CreateMatrix | Generating inputs/outputs doc for: nipype.interfaces.cmtk.cmtk CreateMatrix | ROIGen | Generating inputs/outputs doc for: nipype.interfaces.cmtk.cmtk ROIGen | CFFConverter | Generating inputs/outputs doc for: nipype.interfaces.cmtk.convert CFFConverter | MergeCNetworks | Generating inputs/outputs doc for: nipype.interfaces.cmtk.convert MergeCNetworks | Dcm2nii | Generating inputs/outputs doc for: nipype.interfaces.dcm2nii Dcm2nii | WARNING: Empty - nipype.interfaces.diffusion_toolkit | Info | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.base Info | DTIRecon | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.dti DTIRecon | DTITracker | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.dti DTITracker | HARDIMat | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf HARDIMat | ODFRecon | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf ODFRecon | ODFTracker | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf ODFTracker | SplineFilter | Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.postproc SplineFilter | WARNING: Empty - nipype.interfaces.freesurfer | Info | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.base Info | Binarize | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model Binarize | Concatenate | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model Concatenate | GLMFit | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model GLMFit | Label2Vol | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model Label2Vol | MRISPreproc | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model MRISPreproc | OneSampleTTest | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model OneSampleTTest | SegStats | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model SegStats | ApplyVolTransform | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess ApplyVolTransform | BBRegister | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess BBRegister | DICOMConvert | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess DICOMConvert | FitMSParams | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess FitMSParams | MRIConvert | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess MRIConvert | ParseDICOMDir | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess ParseDICOMDir | ReconAll | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess ReconAll | Resample | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess Resample | RobustRegister | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess RobustRegister | Smooth | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess Smooth | SynthesizeFLASH | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess SynthesizeFLASH | UnpackSDICOMDir | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess UnpackSDICOMDir | ApplyMask | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils ApplyMask | ImageInfo | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils ImageInfo | MRIsConvert | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils MRIsConvert | SampleToSurface | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils SampleToSurface | SurfaceSmooth | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils SurfaceSmooth | SurfaceSnapshots | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils SurfaceSnapshots | SurfaceTransform | Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils SurfaceTransform | test setup | >>> DEBIAN doc building with missing externals >>>: | test teardown | WARNING: Empty - nipype.interfaces.fsl | Info | Generating inputs/outputs doc for: nipype.interfaces.fsl.base Info | BEDPOSTX | FSL environment variables not set | DTIFit | FSL environment variables not set | DistanceMap | FSL environment variables not set | EddyCorrect | FSL environment variables not set | FindTheBiggest | FSL environment variables not set | MakeDyadicVectors | FSL environment variables not set | ProbTrackX | FSL environment variables not set | ProjThresh | FSL environment variables not set | TractSkeleton | FSL environment variables not set | VecReg | FSL environment variables not set | XFibres | FSL environment variables not set | ApplyMask | FSL environment variables not set | ApplyMaskInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths ApplyMaskInput | BinaryMaths | FSL environment variables not set | BinaryMathsInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths BinaryMathsInput | ChangeDataType | FSL environment variables not set | ChangeDataTypeInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths ChangeDataTypeInput | DilateImage | FSL environment variables not set | DilateInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths DilateInput | ErodeImage | FSL environment variables not set | ErodeInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths ErodeInput | IsotropicSmooth | FSL environment variables not set | IsotropicSmoothInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths IsotropicSmoothInput | KernelInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths KernelInput | MathsCommand | FSL environment variables not set | MathsInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MathsInput | MathsOutput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MathsOutput | MeanImage | FSL environment variables not set | MeanImageInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MeanImageInput | MultiImageMaths | FSL environment variables not set | MultiImageMathsInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MultiImageMathsInput | SpatialFilter | FSL environment variables not set | SpatialFilterInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths SpatialFilterInput | TemporalFilter | FSL environment variables not set | TemporalFilterInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths TemporalFilterInput | Threshold | FSL environment variables not set | UnaryMaths | FSL environment variables not set | UnaryMathsInput | Generating inputs/outputs doc for: nipype.interfaces.fsl.maths UnaryMathsInput | Cluster | FSL environment variables not set | ContrastMgr | FSL environment variables not set | FEAT | FSL environment variables not set | FEATModel | FSL environment variables not set | FEATRegister | Generating inputs/outputs doc for: nipype.interfaces.fsl.model FEATRegister | FILMGLS | FSL environment variables not set | FLAMEO | FSL environment variables not set | L2Model | Generating inputs/outputs doc for: nipype.interfaces.fsl.model L2Model | Level1Design | Generating inputs/outputs doc for: nipype.interfaces.fsl.model Level1Design | MELODIC | FSL environment variables not set | MultipleRegressDesign | Generating inputs/outputs doc for: nipype.interfaces.fsl.model MultipleRegressDesign | Randomise | FSL environment variables not set | SMM | FSL environment variables not set | SmoothEstimate | FSL environment variables not set | ApplyWarp | FSL environment variables not set | ApplyXfm | FSL environment variables not set | BET | FSL environment variables not set | FAST | FSL environment variables not set | FLIRT | FSL environment variables not set | FNIRT | FSL environment variables not set | FUGUE | FSL environment variables not set | MCFLIRT | FSL environment variables not set | PRELUDE | FSL environment variables not set | SUSAN | Traceback (most recent call last): | File "../tools/build_interface_docs.py", line 49, in <module> | FSL environment variables not set | SliceTimer | FSL environment variables not set | ConvertXFM | FSL environment variables not set | ExtractROI | docwriter.write_api_docs(outdir) | FSL environment variables not set | File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line 556, in write_api_docs | FilterRegressor | FSL environment variables not set | ImageMaths | FSL environment variables not set | ImageMeants | FSL environment variables not set | ImageStats | FSL environment variables not set | Merge | FSL environment variables not set | Overlay | FSL environment variables not set | PlotMotionParams | FSL environment variables not set | PlotTimeSeries | FSL environment variables not set | PowerSpectrum | FSL environment variables not set | Slicer | self.write_modules_api(modules,outdir) | FSL environment variables not set | File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line 523, in write_modules_api | Smooth | FSL environment variables not set | Split | FSL environment variables not set | SwapDimensions | FSL environment variables not set | >>> DEBIAN doc building with missing externals >>>: add_traits() takes at least 2 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: copytree() takes exactly 2 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: push_file() takes exactly 5 arguments (0 given) | >>> DEBIAN doc building with missing externals >>>: quote_id() takes exactly 1 argument (0 given) | >>> DEBIAN doc building with missing externals >>>: unquote_id() takes exactly 1 argument (0 given) | DataGrabber | Generating inputs/outputs doc for: nipype.interfaces.io DataGrabber | DataSink | Generating inputs/outputs doc for: nipype.interfaces.io DataSink | FreeSurferSource | api_str = self.generate_api_doc(m) | Generating inputs/outputs doc for: nipype.interfaces.io FreeSurferSource | IOBase | File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line 312, in generate_api_doc | Generating inputs/outputs doc for: nipype.interfaces.io IOBase | SQLiteSink | __init__() takes exactly 2 arguments (1 given) | XNATSink | Generating inputs/outputs doc for: nipype.interfaces.io XNATSink | XNATSource | Generating inputs/outputs doc for: nipype.interfaces.io XNATSource | WARNING: Empty - nipype.interfaces.nipy | __import__(uri) | File "/build/nipype-rFhixh/nipype-0.4.1/nipype/interfaces/nipy/__init__.py", line 1, in <module> | from model import FitGLM, EstimateContrast | File "/build/nipype-rFhixh/nipype-0.4.1/nipype/interfaces/nipy/model.py", line 9, in <module> | import nipy.labs.utils.design_matrix as dm | ImportError: No module named design_matrix | make[1]: *** [api] Error 1 -- System Information: Debian Release: wheezy/sid APT prefers unstable APT policy: (990, 'unstable'), (500, 'experimental') Architecture: i386 (x86_64) -- Jakub Wilk -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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