Compilation problem on Fedora

[alcir]

Trying to compile on Fedora 31, I get

...
$ make
Scanning dependencies of target markdown_to_hex
[  1%] Building C object CMakeFiles/markdown_to_hex.dir/utilities/hexdump.c.o
[  2%] Linking C executable markdown_to_hex
[  2%] Built target markdown_to_hex
Scanning dependencies of target markdown_docs
[  3%] Generating markdown_docs.h
[  3%] Built target markdown_docs
Scanning dependencies of target cnd_driver
[  4%] Building CXX object CMakeFiles/cnd_driver.dir/ConvertImageND.cxx.o
In file included from /usr/include/InsightToolkit/itkNumericTraits.h:51,
                 from /usr/include/InsightToolkit/itkConceptChecking.h:32,
                 from /usr/include/InsightToolkit/itkAtomicIntDetail.h:39,
                 from /usr/include/InsightToolkit/itkAtomicInt.h:38,
                 from /usr/include/InsightToolkit/itkTimeStamp.h:33,
                 from /usr/include/InsightToolkit/itkLightObject.h:23,
                 from /usr/include/InsightToolkit/itkObject.h:31,
                 from /usr/include/InsightToolkit/itkRegion.h:31,
                 from /usr/include/InsightToolkit/itkImageRegion.h:31,
                 from /usr/include/InsightToolkit/itkImage.h:21,
                 from /home/user/Downloads/gggg/c3d-git/itkextras/itkOrientedRASImage.h:4,
                 from /home/user/Downloads/gggg/c3d-git/ConvertImageND.h:29,
                 from /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:26:
/usr/include/vxl/vcl/vcl_limits.h:11:5: warning: #warning "This header will be removed in future versions of VXL.  Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py" [-Wcpp]
   11 |   # warning "This header will be removed in future versions of VXL.  Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py"
      |     ^~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In member function ‘int ImageConverter::ProcessCommand(int, char**)’:
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:464:14: error: ‘vcl_acos’ was not declared in this scope
  464 |     adapter(&vcl_acos);
      |              ^~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:517:14: error: ‘vcl_asin’ was not declared in this scope
  517 |     adapter(&vcl_asin);
      |              ^~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:564:14: error: ‘vcl_ceil’ was not declared in this scope
  564 |     adapter(&vcl_ceil);
      |              ^~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:653:14: error: ‘vcl_cos’ was not declared in this scope
  653 |     adapter(&vcl_cos);
      |              ^~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:744:14: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’?
  744 |     adapter(&vcl_exp);
      |              ^~~~~~~
      |              ldexp
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:800:14: error: ‘vcl_floor’ was not declared in this scope
  800 |     adapter(&vcl_floor);
      |              ^~~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1029:14: error: ‘vcl_log’ was not declared in this scope
 1029 |     adapter(&vcl_log);
      |              ^~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1036:14: error: ‘vcl_log10’ was not declared in this scope
 1036 |     adapter(&vcl_log10);
      |              ^~~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1313:11: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’?
 1313 |     exp1(&vcl_exp);
      |           ^~~~~~~
      |           ldexp
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1836:14: error: ‘vcl_sin’ was not declared in this scope
 1836 |     adapter(&vcl_sin);
      |              ^~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1920:14: error: ‘vcl_sqrt’ was not declared in this scope
 1920 |     adapter(&vcl_sqrt);
      |              ^~~~~~~~
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 2]’:
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3094:16:   required from here
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’?
 2469 |         if (!vnl_math_isnan(*q))
      |              ~~~~~~~~~~~~~~^~~~
      |              vnl_math_h_
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 3]’:
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3095:16:   required from here
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’?
 2469 |         if (!vnl_math_isnan(*q))
      |              ~~~~~~~~~~~~~~^~~~
      |              vnl_math_h_
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 4]’:
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3096:16:   required from here
/home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’?
 2469 |         if (!vnl_math_isnan(*q))
      |              ~~~~~~~~~~~~~~^~~~
      |              vnl_math_h_
make[2]: *** [CMakeFiles/cnd_driver.dir/build.make:63: CMakeFiles/cnd_driver.dir/ConvertImageND.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:329: CMakeFiles/cnd_driver.dir/all] Error 2

[pyushkevich]

Which ITK version are you compiling against?

…

On Wed, Nov 13, 2019 at 5:09 PM Alessio ***@***.***> wrote: Trying to compile on Fedora 31, I get ... $ make Scanning dependencies of target markdown_to_hex [ 1%] Building C object CMakeFiles/markdown_to_hex.dir/utilities/hexdump.c.o [ 2%] Linking C executable markdown_to_hex [ 2%] Built target markdown_to_hex Scanning dependencies of target markdown_docs [ 3%] Generating markdown_docs.h [ 3%] Built target markdown_docs Scanning dependencies of target cnd_driver [ 4%] Building CXX object CMakeFiles/cnd_driver.dir/ConvertImageND.cxx.o In file included from /usr/include/InsightToolkit/itkNumericTraits.h:51, from /usr/include/InsightToolkit/itkConceptChecking.h:32, from /usr/include/InsightToolkit/itkAtomicIntDetail.h:39, from /usr/include/InsightToolkit/itkAtomicInt.h:38, from /usr/include/InsightToolkit/itkTimeStamp.h:33, from /usr/include/InsightToolkit/itkLightObject.h:23, from /usr/include/InsightToolkit/itkObject.h:31, from /usr/include/InsightToolkit/itkRegion.h:31, from /usr/include/InsightToolkit/itkImageRegion.h:31, from /usr/include/InsightToolkit/itkImage.h:21, from /home/user/Downloads/gggg/c3d-git/itkextras/itkOrientedRASImage.h:4, from /home/user/Downloads/gggg/c3d-git/ConvertImageND.h:29, from /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:26: /usr/include/vxl/vcl/vcl_limits.h:11:5: warning: #warning "This header will be removed in future versions of VXL. Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py" [-Wcpp] 11 | # warning "This header will be removed in future versions of VXL. Use equivalent C++11 header instead. see: vxl/scripts/UseStandardHeaders.py" | ^~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In member function ‘int ImageConverter::ProcessCommand(int, char**)’: /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:464:14: error: ‘vcl_acos’ was not declared in this scope 464 | adapter(&vcl_acos); | ^~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:517:14: error: ‘vcl_asin’ was not declared in this scope 517 | adapter(&vcl_asin); | ^~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:564:14: error: ‘vcl_ceil’ was not declared in this scope 564 | adapter(&vcl_ceil); | ^~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:653:14: error: ‘vcl_cos’ was not declared in this scope 653 | adapter(&vcl_cos); | ^~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:744:14: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’? 744 | adapter(&vcl_exp); | ^~~~~~~ | ldexp /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:800:14: error: ‘vcl_floor’ was not declared in this scope 800 | adapter(&vcl_floor); | ^~~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1029:14: error: ‘vcl_log’ was not declared in this scope 1029 | adapter(&vcl_log); | ^~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1036:14: error: ‘vcl_log10’ was not declared in this scope 1036 | adapter(&vcl_log10); | ^~~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1313:11: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’? 1313 | exp1(&vcl_exp); | ^~~~~~~ | ldexp /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1836:14: error: ‘vcl_sin’ was not declared in this scope 1836 | adapter(&vcl_sin); | ^~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:1920:14: error: ‘vcl_sqrt’ was not declared in this scope 1920 | adapter(&vcl_sqrt); | ^~~~~~~~ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 2]’: /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3094:16: required from here /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’? 2469 | if (!vnl_math_isnan(*q)) | ~~~~~~~~~~~~~~^~~~ | vnl_math_h_ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 3]’: /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3095:16: required from here /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’? 2469 | if (!vnl_math_isnan(*q)) | ~~~~~~~~~~~~~~^~~~ | vnl_math_h_ /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 4]’: /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:3096:16: required from here /home/user/Downloads/gggg/c3d-git/ConvertImageND.cxx:2469:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_math_h_’? 2469 | if (!vnl_math_isnan(*q)) | ~~~~~~~~~~~~~~^~~~ | vnl_math_h_ make[2]: *** [CMakeFiles/cnd_driver.dir/build.make:63: CMakeFiles/cnd_driver.dir/ConvertImageND.cxx.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:329: CMakeFiles/cnd_driver.dir/all] Error 2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AAJPEWZHMTDFLLUHJKMLZW3QTR3IJA5CNFSM4JNCKTZKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HZEXXQA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJPEW6HEWLCVLPGWUS4EKLQTR3IJANCNFSM4JNCKTZA> .

-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and Science Laboratory Department of Radiology University of Pennsylvania

[alcir]

4.13.1

Thanks.

[pyushkevich]

A couple things: 1. The repo on sourceforge was a couple commits behind the github repo. Please make sure you are using the latest. I just updated sourceforge. 2. I can build using 4.13.2 on my Mac and on Linux. But I compile ITK and C3D with *CMAKE_CXX_FLAGS=-std=c++11*. This may be the difference. Hope this helps!

…

On Thu, Nov 14, 2019 at 11:19 AM Alessio ***@***.***> wrote: 4.13.1 Thanks. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=AAJPEW6RNJSEKDW6AB573GTQTV3C3A5CNFSM4JNCKTZKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEECMYPA#issuecomment-553962556>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJPEW6AFD7UAF3QWERNHFDQTV3C3ANCNFSM4JNCKTZA> .

-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and Science Laboratory Department of Radiology University of Pennsylvania

[alcir]

Thank you very much for the answers.

[alcir]

Unfortunately I'm not a developer, so my skills and knowledge are very limited.
You can see here https://src.fedoraproject.org/rpms/InsightToolkit/blob/master/f/InsightToolkit.spec how ITK was compiled on Fedora.
Maybe there is something preventing compilation of C3D to work?