[Insight-users] Link error compiling ITK
René Sánchez Martín
reny at ctm.ulpgc.es
Thu Jan 12 10:23:15 EST 2006
I have reinstaled the compiler and the system libraries involved in the
previous problem. I have gcc 3.4 now and I have successfully compiled
VTK. However, when I try to compile ITK I get the following error:
Building shared library
/home/reny/CTM/itk/itk2.2-gcc-3.4/bin/libITKBasicFiltersBTcl.so...
`.L8108' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8113' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8118' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8126' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8284' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8289' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8294' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8302' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageItLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8431' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8436' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8441' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8449' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj3EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8585' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8590' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8595' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
`.L8603' referenced in section `.rodata' of
wrap_itkStatisticsImageFilterTcl.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIfLj2EEEE10MakeOutputEj'
of wrap_itkStatisticsImageFilterTcl.o
collect2: ld devolvió el estado de salida 1
make[5]: ***
[/home/reny/CTM/itk/itk2.2-gcc-3.4/bin/libITKBasicFiltersBTcl.so] Error 1
make[4]: *** [default_target] Error 2
make[3]: *** [default_target_BasicFiltersB] Error 2
make[2]: *** [default_target] Error 2
make[1]: *** [default_target_Wrapping_CSwig] Error 2
make: *** [default_target] Error 2
*I tried to disable Wrapping, but then I got a similar error:*
Building executable
/home/reny/CTM/itk/itk2.2-gcc-3.4/bin/itkBasicFiltersTests...
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEES2_E8SetPolesEv'
referenced in section `.rodata' of
itkBSplineResampleImageFunctionTest.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEES2_E8SetPolesEv'
of itkBSplineResampleImageFunctionTest.o
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEENS1_IdLj2EEEE8SetPolesEv'
referenced in section `.rodata' of
itkBSplineResampleImageFunctionTest.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEENS1_IdLj2EEEE8SetPolesEv'
of itkBSplineResampleImageFunctionTest.o
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
referenced in section `.rodata' of
itkBSplineResampleImageFunctionTest.o: defined in discarded section
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
of itkBSplineResampleImageFunctionTest.o
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEdfE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
referenced in section `.rodata' of
itkBSplineResampleImageFunctionTest.o: defined in discarded section
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEdfE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
of itkBSplineResampleImageFunctionTest.o
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIhLj2EEEE10MakeOutputEj'
referenced in section `.rodata' of itkBilateralImageFilterTest3.o:
defined in discarded section
`.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIhLj2EEEE10MakeOutputEj'
of itkBilateralImageFilterTest3.o
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj2EEES2_E8SetPolesEv'
referenced in section `.rodata' of
itkInterpolateImagePointsFilterTest.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj2EEES2_E8SetPolesEv'
of itkInterpolateImagePointsFilterTest.o
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj3EEES2_E8SetPolesEv'
referenced in section `.rodata' of
itkInterpolateImagePointsFilterTest.o: defined in discarded section
`.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj3EEES2_E8SetPolesEv'
of itkInterpolateImagePointsFilterTest.o
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj3EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj3EEERK10vnl_matrixIlERS8_IdEj'
referenced in section `.rodata' of
itkInterpolateImagePointsFilterTest.o: defined in discarded section
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj3EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj3EEERK10vnl_matrixIlERS8_IdEj'
of itkInterpolateImagePointsFilterTest.o
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
referenced in section `.rodata' of
itkInterpolateImagePointsFilterTest.o: defined in discarded section
`.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
of itkInterpolateImagePointsFilterTest.o
collect2: ld devolvió el estado de salida 1
make[7]: ***
[/home/reny/CTM/itk/itk2.2-gcc-3.4/bin/itkBasicFiltersTests] Error 1
make[6]: *** [default_target] Error 2
make[5]: *** [default_target_BasicFilters] Error 2
make[4]: *** [default_target] Error 2
make[3]: *** [default_target_Code] Error 2
make[2]: *** [default_target] Error 2
make[1]: *** [default_target_Testing] Error 2
make: *** [default_target] Error 2
Any idea?
Thanks in advance.
Luis Ibanez escribió:
>
> Hi Rene,
>
> It seems that you have a misconfigured Linux system.
>
> You may want ot reinstall your Linux system before you continue
> experimenting with ITK.
>
> There is not much that we can do to help you if your compiler
> and system libraries are not installed correctly.
>
>
> Have you tried building any other large size project in that
> machine ?
>
> VTK for example ?
>
>
> BTW, note that GCC compiled code is not necesarily portable
> across different versions of compilers. So, you shouldn't
> expect code compiled for gcc 3.3 to be linkable with code
> compiled with gcc 4.0. Most of the time it may work fine,
> but the name mangling is not guaranteed to be stable accross
> versions. All that to say, that part of the problem may be
> that you may be mixing versions of gcc when building ITK
> and your application.
>
>
>
> Regards,
>
>
> Luis
>
>
> -----------------------------
> René Sánchez Martín wrote:
>
>> Dear ITK users:
>>
>> About one or two months ago I compiled ITK 2.4 with gcc 4.0 in the
>> server of our lab. I tested it with some code and everything was
>> fine. Two weeks ago, one of my partners in the lab started to use
>> ITK. Last week, he had strange errors at execution time related to
>> glibc:
>>
>> *** glibc detected *** free(): invalid pointer: 0x083b0c68 ***
>>
>>
>> The code compiled but it crashed at execution time. The code was
>> pretty simple, (it just read and image), so I suspected that the
>> problem was rather related to ITK installation than the code itself.
>> I take the code and tried in my laptop, and the result was the same.
>> I suspected it was a problem with a system library (maybe
>> libstdc++-libc6?) and I tried to compiled again and execute some code
>> I have tested thousands of times in my own laptop and it didn't
>> worked, neither in the server nor in my laptop. I am using Debian and
>> I strongly believe that it is a problem with a package I updated in
>> both machines (apt-get dist-upgrade).
>>
>> I tried to use more stable versions of gcc (gcc 3.4) and ITK (2.2) to
>> solve the problem. I tried to compile ITK 2.2 and I had the following
>> error:
>>
>> Building object file itkMaskImageFilterTest.o...
>> Building object file itkMaskNegatedImageFilterTest.o...
>> Building object file itkMathematicalMorphologyImageFilterTest.o...
>> Building object file itkMaximumImageFilterTest.o...
>> Building object file itkMeanImageFilterTest.o...
>> Building object file itkMedianImageFilterTest.o...
>> Building object file itkMinimumImageFilterTest.o...
>> Building object file itkMinimumMaximumImageCalculatorTest.o...
>> Building object file itkMinimumMaximumImageFilterTest.o...
>> Building object file itkMirrorPadImageTest.o...
>> Building object file itkMultiplyImageFilterTest.o...
>> Building executable /home/dario/itk/itk2.2/bin/itkBasicFiltersTests...
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEES2_E8SetPolesEv'
>> referenced in section `.rodata' of
>> itkBSplineResampleImageFunctionTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEES2_E8SetPolesEv'
>> of itkBSplineResampleImageFunctionTest.o
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEENS1_IdLj2EEEE8SetPolesEv'
>> referenced in section `.rodata' of
>> itkBSplineResampleImageFunctionTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIfLj2EEENS1_IdLj2EEEE8SetPolesEv'
>> of itkBSplineResampleImageFunctionTest.o
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEddE2:
>>
>> 3SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> referenced in section `.rodata' of
>> itkBSplineResampleImageFunctionTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> of itkBSplineResampleImageFunctionTest.o
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEdfE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> referenced in section `.rodata' of
>> itkBSplineResampleImageFunctionTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIfLj2EEEdfE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> of itkBSplineResampleImageFunctionTest.o
>> `.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIhLj2EEEE10MakeOutputEj'
>> referenced in section `.rodata' of itkBilateralImageFilterTest3.o:
>> defined in
>> discarded section
>> `.gnu.linkonce.t._ZN3itk21StatisticsImageFilterINS_5ImageIhLj2EEEE10MakeOutputEj'
>> of itkBilateralImageFilterTest3.o
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj2EEES2_E8SetPolesEv'
>> referenced in section `.rodata' of
>> itkInterpolateImagePointsFilterTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj2EEES2_E8SetPolesEv'
>> of itkInterpolateImagePointsFilterTest.o
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositionImageFilterINS_5ImageIdLj3EEES2_E8SetPolesEv'
>> referenced in section `.rodata' of
>> itkInterpolateImagePointsFilterTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZN3itk31BSplineDecompositio:
>> nImageFilterINS_5ImageIdLj3EEES2_E8SetPolesEv' of
>> itkInterpolateImagePointsFilterTest.o
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj3EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj3EEERK10vnl_matrixIlERS8_IdEj'
>> referenced in section `.rodata' of
>> itkInterpolateImagePointsFilterTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj3EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj3EEERK10vnl_matrixIlERS8_IdEj'
>> of itkInterpolateImagePointsFilterTest.o
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> referenced in section `.rodata' of
>> itkInterpolateImagePointsFilterTest.o: defined in discarded section
>> `.gnu.linkonce.t._ZNK3itk31BSplineInterpolateImageFunctionINS_5ImageIdLj2EEEddE23SetInterpolationWeightsERKNS_15ContinuousIndexIdLj2EEERK10vnl_matrixIlERS8_IdEj'
>> of itkInterpolateImagePointsFilterTest.o
>> collect2: ld devolvió el estado de salida 1
>> make[7]: *** [/home/dario/itk/itk2.2/bin/itkBasicFiltersTests] Error 1
>> make[6]: *** [default_target] Error 2
>> make[5]: *** [default_target_BasicFilters] Error 2
>> make[4]: *** [default_target] Error 2
>> make[3]: *** [default_target_Code] Error 2
>> make[2]: *** [default_target] Error 2
>> make[1]: *** [default_target_Testing] Error 2
>> make: *** [default_target] Error 2
>>
>>
>> I need to use ITK. I don't care if it is the 2.4 I have already
>> compiled but doesn't seem to work in execution time or if it is the
>> version I tried to compile. Any sugestion to get a solution?
>>
>> Thanks in advance.
>>
>> Rene Sanchez.
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>>
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