Bug#586247: python-vigra: segmentation fault in vigra::detail::noiseVarianceListMedianCut

[Jakub Wilk]

Package: python-vigra
Version: 1.7.0+dfsg-3
Severity: serious
Justification: FTBFS



import numpy
import vigra.noise
import vigra.arraytypes
image = vigra.arraytypes.ScalarImage(numpy.random.rand(100,100)*255, 
dtype=numpy.float32)
vigra.noise.noiseVarianceClustering(image)

Severity serious, because the bug is causing build failures.

gdb traceback:


    at 
/tmp/buildd/libvigraimpex-1.7.0+dfsg/include/vigra/noise_normalization.hxx:1119

    at 
/tmp/buildd/libvigraimpex-1.7.0+dfsg/include/vigra/noise_normalization.hxx:1128

#6  boost::python::detail::caller_arity<8u>::impl<vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, 
vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, 
vigra::StridedArrayTag>), boost::python::default_call_policies, boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, 
vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, 
vigra::Multiband<float>, vigra::StridedArrayTag> > >::operator() (this=<value optimized out>, args_=<value optimized out>)
    at /usr/include/boost/python/detail/caller.hpp:223
#7  0x00007f591d405c1e in boost::python::objects::py_function::operator() (this=<value 
optimized out>, args=0x29f9b10, keywords=<value optimized out>)
    at ./boost/python/object/py_function.hpp:143
#8  boost::python::objects::function::call (this=<value optimized out>, 
args=0x29f9b10, keywords=<value optimized out>)
    at libs/python/src/object/function.cpp:226
#9  0x00007f591d405ec8 in operator() (function_obj_ptr=<value optimized out>) 
at libs/python/src/object/function.cpp:585
#10 invoke (function_obj_ptr=<value optimized out>) at 
./boost/function/function_template.hpp:188
#11 0x00007f591d40d52b in boost::function0<void>::operator() (f=DWARF-2 
expression error: DW_OP_reg operations must be used either alone or in conjuction 
with DW_OP_piece.
) at ./boost/function/function_template.hpp:1013
#12 boost::python::handle_exception_impl (f=DWARF-2 expression error: DW_OP_reg 
operations must be used either alone or in conjuction with DW_OP_piece.
) at libs/python/src/errors.cpp:25
#13 0x00007f591d4027b8 in 
handle_exception<boost::python::objects::<unnamed>::bind_return> (func=<value 
optimized out>, args=0x29f9b10, kw=0xffffffff0)
    at ./boost/python/errors.hpp:29
#14 function_call (func=<value optimized out>, args=0x29f9b10, kw=0xffffffff0) 
at libs/python/src/object/function.cpp:626
#15 0x0000000000418493 in PyObject_Call (func=0x1, arg=0x29f9b10, 
kw=0xffffffff0) at ../Objects/abstract.c:1861
#16 0x000000000048f62e in do_call (f=0x2712f90, throwflag=<value optimized 
out>) at ../Python/ceval.c:3823
#17 call_function (f=0x2712f90, throwflag=<value optimized out>) at 
../Python/ceval.c:3635
#18 PyEval_EvalFrameEx (f=0x2712f90, throwflag=<value optimized out>) at 
../Python/ceval.c:2304

#20 0x0000000000491722 in PyEval_EvalCode (co=0x1, globals=0x29f9b10, 
locals=0xffffffff0) at ../Python/ceval.c:514

#23 0x00000000004b103b in PyRun_SimpleFileExFlags (fp=0x26f8010, filename=0x7fffde7f9d14 
"test2.py", closeit=1, flags=0x7fffde7f8790)
    at ../Python/pythonrun.c:879
#24 0x0000000000414633 in Py_Main (argc=1, argv=<value optimized out>) at 
../Modules/main.c:532

#26 0x0000000000413a29 in _start ()


-- System Information:
Debian Release: squeeze/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=pl_PL.UTF-8 (charmap=ANSI_X3.4-1968) (ignored: LC_ALL 
set to C)
Shell: /bin/sh linked to /bin/dash

Versions of packages python-vigra depends on:
ii  libboost-python1.42.0     1.42.0-3       Boost.Python Library
ii  libc6                     2.11.2-1       Embedded GNU C Library: Shared lib
ii  libfftw3-3                3.2.2-1        library for computing Fast Fourier
ii  libgcc1                   1:4.4.4-5      GCC support library

ii  libvigraimpex2ldbl        1.7.0+dfsg-3   C++ computer vision library
ii  python                    2.5.4-9        An interactive high-level object-o
ii  python-numpy              1:1.3.0-3+b1   Numerical Python adds a fast array
ii  python-support            1.0.8          automated rebuilding support for P

Versions of packages python-vigra recommends:
pn  python-h5py                   <none>     (no description available)
pn  python-qt4                    <none>     (no description available)

Versions of packages python-vigra suggests:

--
Jakub Wilk

This Python program causes non-deterministic segmentation faults on AMD64: #0 0x00007f591a68b64c in vigra::detail::noiseVarianceListMedianCut<vigra::ArrayVector<vigra::TinyVector<double, 2>, std::allocator<vigra::TinyVector<double, 2> > >, vigra::ArrayVector<vigra::TinyVector<unsigned int, 2>, std::allocator<vigra::TinyVector<unsigned int, 2> > > > (noise=..., clusters=..., maxClusterCount=<value optimized out>) at /tmp/buildd/libvigraimpex-1.7.0+dfsg/include/vigra/noise_normalization.hxx:585 #1 0x00007f591a68d9ea in vigra::detail::noiseVarianceClusteringImpl<vigra::ArrayVector<vigra::TinyVector<double, 2>, std::allocator<vigra::TinyVector<double, 2> > >, std::vector<vigra::TinyVector<double, 2>, std::allocator<vigra::TinyVector<double, 2> > > > (noise=..., result=..., clusterCount=10, quantile=<value optimized out>) at /tmp/buildd/libvigraimpex-1.7.0+dfsg/include/vigra/noise_normalization.hxx:716 #2 0x00007f591a697c45 in noiseVarianceClustering<vigra::ConstStridedImageIterator<float>, vigra::StandardConstValueAccessor<float>, std::vector<vigra::TinyVector<double, 2>, std::allocator<vigra::TinyVector<double, 2> > > > (image=<value optimized out>, useGradient=<value optimized out>, windowRadius=<value optimized out>, clusterCount=<value optimized out>, averagingQuantile=<value optimized out>, noiseEstimationQuantile=<value optimized out>, noiseVarianceInitialGuess=<value optimized out>, res=<value optimized out>) #3 noiseVarianceClustering<vigra::ConstStridedImageIterator<float>, vigra::StandardConstValueAccessor<float>, std::vector<vigra::TinyVector<double, 2>, std::allocator<vigra::TinyVector<double, 2> > > > (image=<value optimized out>, useGradient=<value optimized out>, windowRadius=<value optimized out>, clusterCount=<value optimized out>, averagingQuantile=<value optimized out>, noiseEstimationQuantile=<value optimized out>, noiseVarianceInitialGuess=<value optimized out>, res=<value optimized out>) #4 vigra::pythonNoiseVarianceClustering<float> (image=<value optimized out>, useGradient=<value optimized out>, windowRadius=<value optimized out>, clusterCount=<value optimized out>, averagingQuantile=<value optimized out>, noiseEstimationQuantile=<value optimized out>, noiseVarianceInitialGuess=<value optimized out>, res=<value optimized out>) at /tmp/buildd/libvigraimpex-1.7.0+dfsg/vigranumpy/src/core/noise.cxx:89 #5 0x00007f591a690b55 in invoke<boost::python::detail::caller_arity<4u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector5<vigra::NumpyAnyArray, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::result_converter, vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t0, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t1, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t2, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t3, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t4, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t5, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t6, boost::python::detail::caller_arity<8u>::impl<F, Policies, Sig>::operator()(PyObject*, PyObject*) [with F = vigra::NumpyAnyArray (*)(vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag>), Policies = boost::python::default_call_policies, Sig = boost::mpl::vector9<vigra::NumpyAnyArray, vigra::NumpyArray<2u, vigra::Singleband<float>, vigra::StridedArrayTag>, bool, unsigned int, unsigned int, double, double, double, vigra::NumpyArray<3u, vigra::Multiband<float>, vigra::StridedArrayTag> >]::c_t7> (this=<value optimized out>, args_=<value optimized out>) at /usr/include/boost/python/detail/invoke.hpp:75 #19 0x00000000004915f9 in PyEval_EvalCodeEx (co=0x7f5922114468, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=44014448, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2875 #21 0x00000000004b0e9b in run_mod (fp=<value optimized out>, filename=0x7fffde7f9d14 "test2.py", start=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, closeit=1, flags=0x7fffde7f8790) at ../Python/pythonrun.c:1273 #22 PyRun_FileExFlags (fp=<value optimized out>, filename=0x7fffde7f9d14 "test2.py", start=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, closeit=1, flags=0x7fffde7f8790) at ../Python/pythonrun.c:1259 #25 0x00007f5921329c4d in __libc_start_main (main=<value optimized out>, argc=<value optimized out>, ubp_av=<value optimized out>, init=<value optimized out>, fini=<value optimized out>, rtld_fini=<value optimized out>, stack_end=0x7fffde7f88a8) at libc-start.c:228 ii libhdf5-serial-1.8.4 [lib 1.8.4-patch1-2 Hierarchical Data Format 5 (HDF5) ii libstdc++6 4.4.4-5 The GNU Standard C++ Library v3 ii python-vigra-doc 1.7.0+dfsg-3 Documentation for Python bindings

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