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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

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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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