pyushkevich
commented
3 years ago Hi,
Are you building using ITKv5? If so, there is the itk5 branch of c3d that you should checkout using git. The master branch only builds against ITKv4 (for now, I will probably merge soon).
Thanks, Paul
On Mon, Mar 29, 2021 at 9:25 AM cepa995 @.***> wrote:
I am trying to build C3D on Ubuntu 20.04 and I am using latest ITK version for it. But once I configure the build and try to make -j5 I get following error:
@.***VirtualBox:~/c3d_test/c3d/build$ export CMAKE_PREFIX_PATH=$HOME/c3d_test/itk-c3d-install/usr/local
@.***VirtualBox:~/c3d_test/c3d/build$ cmake ..
-- CPACK_SYSTEM_NAME Linux-x86_64
-- CPACK_PACKAGE_FILE_NAME c3d-1.1.0-Linux-x86_64
-- Configuring done
-- Generating done
-- Build files have been written to: /home/stefan/c3d_test/c3d/build
@.***VirtualBox:~/c3d_test/c3d/build$ make -j5
Scanning dependencies of target ITKVoxBoIO
Scanning dependencies of target markdown_to_hex
Scanning dependencies of target cnd_maxflow
Scanning dependencies of target cnd_adapters
Scanning dependencies of target ITKPovRayIO
[ 1%] Building C object CMakeFiles/markdown_to_hex.dir/utilities/hexdump.c.o
[ 2%] Building CXX object CMakeFiles/cnd_maxflow.dir/external/GCv2p3/GCoptimization.cpp.o
[ 3%] Building CXX object itkextras/VoxBoIO/CMakeFiles/ITKVoxBoIO.dir/itkVoxBoCUBImageIO.cxx.o
[ 3%] Building CXX object itkextras/PovRayIO/CMakeFiles/ITKPovRayIO.dir/itkPovRayDF3ImageIO.cxx.o
[ 4%] Linking C executable markdown_to_hex
[ 4%] Built target markdown_to_hex
Scanning dependencies of target cnd_api
[ 5%] Building CXX object CMakeFiles/cnd_api.dir/api/ConvertAPI.cxx.o
[ 6%] Building CXX object CMakeFiles/cnd_maxflow.dir/external/GCv2p3/LinkedBlockList.cpp.o
[ 6%] Building CXX object CMakeFiles/cnd_maxflow.dir/external/GCv2p3/graph.cpp.o
[ 7%] Building CXX object CMakeFiles/cnd_maxflow.dir/external/GCv2p3/maxflow.cpp.o
[ 8%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/AddImages.cxx.o
[ 9%] Linking CXX static library libcnd_maxflow.a
[ 9%] Built target cnd_maxflow
[ 10%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/AlignByLandmarks.cxx.o
[ 11%] Building CXX object itkextras/PovRayIO/CMakeFiles/ITKPovRayIO.dir/itkPovRayDF3ImageIOFactory.cxx.o
[ 11%] Linking CXX static library libcnd_api.a
[ 11%] Built target cnd_api
Scanning dependencies of target markdown_docs
[ 12%] Generating markdown_docs.h
[ 13%] Building CXX object itkextras/VoxBoIO/CMakeFiles/ITKVoxBoIO.dir/itkVoxBoCUBImageIOFactory.cxx.o
[ 13%] Built target markdown_docs
[ 13%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/AntiAliasImage.cxx.o
[ 14%] Linking CXX static library libITKPovRayIO.a
[ 14%] Built target ITKPovRayIO
Scanning dependencies of target cnd_driver
[ 15%] Building CXX object CMakeFiles/cnd_driver.dir/ConvertImageND.cxx.o
[ 16%] Linking CXX static library libITKVoxBoIO.a
[ 16%] Built target ITKVoxBoIO
[ 17%] Building CXX object CMakeFiles/cnd_driver.dir/utilities/doc/Documentation.cxx.o
[ 18%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/ApplyMetric.cxx.o
[ 19%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/BinaryHoleFill.cxx.o
/home/stefan/c3d_test/c3d/ConvertImageND.cxx: In member function ‘int ImageConverter<TPixel, VDim>::ProcessCommand(int, char**)’:
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:463:14: error: ‘vcl_acos’ was not declared in this scope
463 | adapter(&vcl_acos);
| ^~~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx:516:14: error: ‘vcl_asin’ was not declared in this scope
516 | adapter(&vcl_asin);
| ^~~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx:645:14: error: ‘vcl_cos’ was not declared in this scope
645 | adapter(&vcl_cos);
| ^~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx:736:14: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’?
736 | adapter(&vcl_exp);
| ^~~~~~~ | ldexp/home/stefan/c3d_test/c3d/ConvertImageND.cxx:1005:14: error: ‘vcl_log’ was not declared in this scope
1005 | adapter(&vcl_log);
| ^~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx:1012:14: error: ‘vcl_log10’ was not declared in this scope
1012 | adapter(&vcl_log10);
| ^~~~~~~~~/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx: In member function ‘double ApplyMetric<TPixel, VDim>::GetValueInternalSymmetric(ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::TransformPointer, ApplyMetric<TPixel, VDim>::TransformPointer, const char*)’:
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:446:33: error: there are no arguments to ‘vcl_sqrt’ that depend on a template parameter, so a declaration of ‘vcl_sqrt’ must be available [-fpermissive]
446 | const double denom = -1.0 vcl_sqrt(sff smm );
| ^~~~~~~~/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:446:33: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:1257:11: error: ‘vcl_exp’ was not declared in this scope; did you mean ‘ldexp’?
1257 | exp1(&vcl_exp);
| ^~~~~~~ | ldexp/home/stefan/c3d_test/c3d/ConvertImageND.cxx:1753:14: error: ‘vcl_sin’ was not declared in this scope
1753 | adapter(&vcl_sin);
| ^~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx:1837:14: error: ‘vcl_sqrt’ was not declared in this scope
1837 | adapter(&vcl_sqrt);
| ^~~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx: In member function ‘int ImageConverter<TPixel, VDim>::ProcessCommandLine(int, char**)’:
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2143:8: error: ‘itk::MultiThreader’ has not been declared
2143 | itk::MultiThreader::SetGlobalDefaultNumberOfThreads(1);
| ^~~~~~~~~~~~~/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx: In instantiation of ‘double ApplyMetric<TPixel, VDim>::GetValueInternalSymmetric(ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::TransformPointer, ApplyMetric<TPixel, VDim>::TransformPointer, const char*) [with TPixel = double; unsigned int VDim = 2; ApplyMetric<TPixel, VDim>::ImagePointer = itk::SmartPointer<itk::OrientedRASImage<double, 2> >; ApplyMetric<TPixel, VDim>::TransformPointer = itk::SmartPointer<itk::AffineTransform<double, 2> >]’:
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:468:16: required from here
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:446:41: error: ‘vcl_sqrt’ was not declared in this scope
446 | const double denom = -1.0 vcl_sqrt(sff smm );
| ~~~~~~~~^~~~~~~~~~~~/home/stefan/c3d_test/c3d/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter<TPixel, VDim>::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 2]’:
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2959:16: required from here
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2386:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_mathh’?
2386 | if (!vnl_math_isnan(*q))
| ~~~~~~~~~~~~~~^~~~ | vnl_math_h_/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx: In instantiation of ‘double ApplyMetric<TPixel, VDim>::GetValueInternalSymmetric(ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::TransformPointer, ApplyMetric<TPixel, VDim>::TransformPointer, const char*) [with TPixel = double; unsigned int VDim = 3; ApplyMetric<TPixel, VDim>::ImagePointer = itk::SmartPointer<itk::OrientedRASImage<double, 3> >; ApplyMetric<TPixel, VDim>::TransformPointer = itk::SmartPointer<itk::AffineTransform<double, 3> >]’:
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:469:16: required from here
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:446:41: error: ‘vcl_sqrt’ was not declared in this scope
/home/stefan/c3d_test/c3d/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter<TPixel, VDim>::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 3]’:
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2960:16: required from here
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2386:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_mathh’?
2386 | if (!vnl_math_isnan(*q))
| ~~~~~~~~~~~~~~^~~~ | vnl_math_h_/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx: In instantiation of ‘double ApplyMetric<TPixel, VDim>::GetValueInternalSymmetric(ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::ImagePointer, ApplyMetric<TPixel, VDim>::TransformPointer, ApplyMetric<TPixel, VDim>::TransformPointer, const char*) [with TPixel = double; unsigned int VDim = 4; ApplyMetric<TPixel, VDim>::ImagePointer = itk::SmartPointer<itk::OrientedRASImage<double, 4> >; ApplyMetric<TPixel, VDim>::TransformPointer = itk::SmartPointer<itk::AffineTransform<double, 4> >]’:
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:470:16: required from here
/home/stefan/c3d_test/c3d/adapters/ApplyMetric.cxx:446:41: error: ‘vcl_sqrt’ was not declared in this scope
/home/stefan/c3d_test/c3d/ConvertImageND.cxx: In instantiation of ‘TPixel ImageConverter<TPixel, VDim>::ReadIntensityValue(const char*) [with TPixel = double; unsigned int VDim = 4]’:
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2961:16: required from here
/home/stefan/c3d_test/c3d/ConvertImageND.cxx:2386:28: error: ‘vnl_math_isnan’ was not declared in this scope; did you mean ‘vnl_mathh’?
2386 | 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/Makefile2:482: CMakeFiles/cnd_driver.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 20%] Building CXX object CMakeFiles/cnd_adapters.dir/adapters/BiasFieldCorrectionN4.cxx.o
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx: In member function ‘void BiasFieldCorrectionN4<TPixel, VDim>::operator()()’:
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:71:7: error: there are no arguments to ‘vcl_ceil’ that depend on a template parameter, so a declaration of ‘vcl_ceil’ must be available [-fpermissive]
71 | vcl_ceil( domain / splineDistance ) );
| ^~~~~~~~/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:71:7: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx: In instantiation of ‘void BiasFieldCorrectionN4<TPixel, VDim>::operator()() [with TPixel = double; unsigned int VDim = 2]’:
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:225:16: required from here
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:71:15: error: ‘vcl_ceil’ was not declared in this scope
71 | vcl_ceil( domain / splineDistance ) );
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx: In instantiation of ‘void BiasFieldCorrectionN4<TPixel, VDim>::operator()() [with TPixel = double; unsigned int VDim = 3]’:
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:226:16: required from here
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:71:15: error: ‘vcl_ceil’ was not declared in this scope
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx: In instantiation of ‘void BiasFieldCorrectionN4<TPixel, VDim>::operator()() [with TPixel = double; unsigned int VDim = 4]’:
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:227:16: required from here
/home/stefan/c3d_test/c3d/adapters/BiasFieldCorrectionN4.cxx:71:15: error: ‘vcl_ceil’ was not declared in this scope
make[2]: *** [CMakeFiles/cnd_adapters.dir/build.make:102: CMakeFiles/cnd_adapters.dir/adapters/ApplyMetric.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/cnd_adapters.dir/build.make:128: CMakeFiles/cnd_adapters.dir/adapters/BiasFieldCorrectionN4.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:787: CMakeFiles/cnd_adapters.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
Is this caused due to using wrong compiler or ITK version, or perhaps something else?
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/c3d/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW4A5T7YFJVH36L2Z6LTGCEWZANCNFSM4Z7SZAXA .
-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine
cepa995
carandraug
I am trying to build C3D on Ubuntu 20.04 and I am using latest ITK version for it. But once I configure the build and try to
make -j5I get following error:Is this caused due to using wrong compiler or ITK version, or perhaps something else?