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Hi Thomas,

I just checked in a patch to the ITK dependency that may fix your build
error. Can you try configuring and building again from a clean build
directory?

Thanks,

Ayla

> On Mar 23, 2017, at 1:49 AM, Thomas Engels
> <thomas.engels@mail.tu-berlin.de> wrote:
>
> Dear all,
>
> I am sorry for yesterdays email, I had not unset $MAKEFLAGS which is why
> I did not see the actual error. The problem seems to be an
> incompatibility with gcc:
>
>
> [ 2%] Building CXX object
> Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o
> cd
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl
> && /usr/bin/c++
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external/fftw/include
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/v3p/netlib
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/core
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external/Modules/ThirdParty/VNL/src/vxl/v3p/netlib
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl
> -I/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external/Modules/ThirdParty/VNL/src/vxl/core
>
> -std=c++11 -Wall -fpermissive -Wall -Wcast-align
> -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch
> -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings
> -funit-at-a-time -Wno-strict-overflow -Wno-unused-local-typedefs
> -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual
> -Wstrict-null-sentinel -msse2 -w -w -O2 -DNDEBUG -o
> CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o -c
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_deprecated.cxx
> In file included from
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_iosfwd.h:8:0,
> from
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_iostream.h:27,
> from
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_deprecated.cxx:4:
> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/ITK_external/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h:137:4:
> error: #error "Dunno about this gcc"
> # error "Dunno about this gcc"
> ^~~~~
> Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/build.make:65:
> recipe for target
> 'Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o'
> failed
> make[5]: ***
> [Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o]
> Error 1
> make[5]: Leaving directory
> '/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external'
> CMakeFiles/Makefile2:597: recipe for target
> 'Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/all' failed
> make[4]: ***
> [Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/all] Error 2
> make[4]: Leaving directory
> '/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external'
> Makefile:130: recipe for target 'all' failed
> make[3]: *** [all] Error 2
> make[3]: Leaving directory
> '/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Build/ITK_external'
> CMakeFiles/ITK_external.dir/build.make:114: recipe for target
> 'Externals/Stamp/ITK_external/ITK_external-build' failed
> make[2]: *** [Externals/Stamp/ITK_external/ITK_external-build] Error 2
> make[2]: Leaving directory '/home/tengels/bin/Seg3D-2.3.2/bin'
> CMakeFiles/Makefile2:339: recipe for target
> 'CMakeFiles/ITK_external.dir/all' failed
> make[1]: *** [CMakeFiles/ITK_external.dir/all] Error 2
> make[1]: Leaving directory '/home/tengels/bin/Seg3D-2.3.2/bin'
> Makefile:86: recipe for target 'all' failed
> make: *** [all] Error 2
> Building Seg3D returned an error
>
> Either the code failed to build properly or
>
> the testing programs failed to complete without
>
> every single test program passing the test.
>
>
> [...]
>
> my gcc is version 6.3.1
>
> is it possible to skip the compilation for this file (which is called
> deprecated anyhow) ?
>
> thanks for your help
>
>
>
>
> On 22.03.2017 18:22, Thomas Engels wrote:
>> Dear Madam or Sir,
>>
>> I'm trying to install Seg3D on my fedora 24 workstation, and failing as
>> you may guess from the fact that I write an email.
>>
>> I have qt-devel 4.8.7 installed, as well as CMake. Following your
>> instructions I hit
>>
>> cmake ../Superbuild
>>
>> in the bin/ folder, followed by make or gmake. Both fail at the same point:
>>
>>
>> [...]
>>
>> Writing grammar tables to
>> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Install/Python_external/lib/python3.4/lib2to3/PatternGrammar3.4.3.final.0.pickle
>> if test "xno" != "xno" ; then \
>> case no in \
>> upgrade) ensurepip="--upgrade" ;; \
>> install|*) ensurepip="" ;; \
>> esac; \
>>
>> LD_LIBRARY_PATH=/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/Python_external:/usr/lib64/mpich/lib
>> ./python -E -m ensurepip \
>> $ensurepip --root=/ ; \
>> fi
>> make[3]: Leaving directory
>> '/home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/Python_external'
>> cd /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Source/Python_external &&
>> /usr/bin/cmake -E touch
>> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Stamp/Python_external/Python_external-install
>> [ 52%] Completed 'Python_external'
>> /usr/bin/cmake -E make_directory
>> /home/tengels/bin/Seg3D-2.3.2/bin/CMakeFiles
>> /usr/bin/cmake -E touch
>> /home/tengels/bin/Seg3D-2.3.2/bin/CMakeFiles/Python_external-complete
>> /usr/bin/cmake -E touch
>> /home/tengels/bin/Seg3D-2.3.2/bin/Externals/Stamp/Python_external/Python_external-done
>> make[2]: Leaving directory '/home/tengels/bin/Seg3D-2.3.2/bin'
>> [ 55%] Built target Python_external
>> make[1]: Leaving directory '/home/tengels/bin/Seg3D-2.3.2/bin'
>> Makefile:86: recipe for target 'all' failed
>> make: *** [all] Error 2
>> Building Seg3D returned an error
>>
>> Either the code failed to build properly or
>>
>> the testing programs failed to complete without
>>
>> every single test program passing the test.
>>
>> [...]
>>
>> The above output was generated by ./build.sh --verbose
>>
>> Do you have any advice what might go wrong?
>>
>> Regards
>>
>> Thomas
>>
>>
>
> --
> Thomas Engels, Ph.D.
> Postdoctoral Researcher
> AIFIT Project (Flying insects in turbulence)
> http://aifit.cfd.tu-berlin.de
>
> Institut für Strömungsmechanik und Technische Akustik
> FG Numerische Fluiddynamik (MB123)
> Müller-Breslau-Strasse 8
> 10623 Berlin
> Germany
> +49 30 314 22849
>
> École normale supérieure
> Laboratoire de Météorologie Dynamique
> 24, Rue Lhomond
> 75231 Paris Cedex 05
> France
>
> _______________________________________________
> Seg3d mailing list: Seg3d@sci.utah.edu
> http://www.sci.utah.edu/software/seg3d.html
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> in the message body.

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• [Seg3D] Seg3D install on linux/fedora, Thomas Engels, 03/22/2017
  • Re: [Seg3D] Seg3D install on linux/fedora, Thomas Engels, 03/23/2017
    • Re: [Seg3D] Seg3D install on linux/fedora, Ayla Khan, 03/23/2017

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