[SOLVED] Failing to build CGAL plugin

[Owen]

Hi SOFA community,

SOFA used to work smoothly on my computer but I had to rebuild SOFA today as I upgraded my OS to Ubuntu 20.04. Then I encountered a problem that I cannot build CGAL plugin while the rest of SOFA works fine.

A part of the command line outputs is below:

[13/19] Building CXX object applications/plugins/CGALPlugin/CMakeFiles/CGALPlugin.dir/initCGALPlugin.cpp.o
FAILED: applications/plugins/CGALPlugin/CMakeFiles/CGALPlugin.dir/initCGALPlugin.cpp.o 
/usr/bin/c++  -DCGALPlugin_EXPORTS -DCGAL_MESH_3_VERBOSE=0 -DNDEBUG -Iinclude -I/home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin -I/home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/.. -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/src -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/../SofaSimulationCore/src -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/../SofaDefaultType/src -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/../SofaCore/src -I/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen -I/home/owen/Softwares/sofa/src/SofaKernel/extlibs/json -I/home/owen/Softwares/sofa/src/extlibs/gtest/include -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaDefaultType/src -I/home/owen/Softwares/sofa/src/SofaKernel/SofaSimulation/../modules -I/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaSimulationCore/src -I/home/owen/Softwares/sofa/src/applications/plugins/CImgPlugin/src -I/home/owen/Softwares/sofa/src/applications/plugins/CImgPlugin/extlibs/CImg/.. -Wall -W -O3 -DNDEBUG -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -fPIC   -DSOFA_BUILD_CGALPLUGIN -DFRAMEWORK_TEST_RESOURCES_DIR=\"/home/owen/Softwares/sofa/src/SofaKernel/SofaFramework/resources/tests\" -pthread -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dcimg_use_tiff -Dcimg_use_jpeg -Dcimg_use_png -DPNG_SKIP_SETJMP_CHECK -Dcimg_no_system_calls -std=gnu++11 -MD -MT applications/plugins/CGALPlugin/CMakeFiles/CGALPlugin.dir/initCGALPlugin.cpp.o -MF applications/plugins/CGALPlugin/CMakeFiles/CGALPlugin.dir/initCGALPlugin.cpp.o.d -o applications/plugins/CGALPlugin/CMakeFiles/CGALPlugin.dir/initCGALPlugin.cpp.o -c /home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/initCGALPlugin.cpp
In file included from /home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/Core:326,
                 from /home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/SparseCore:4,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/src/sofa/helper/StateMask.h:27,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src/sofa/core/behavior/BaseMechanicalState.h:31,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src/sofa/core/behavior/MechanicalState.h:25,
                 from /home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/MeshGenerationFromPolyhedron.h:37,
                 from /home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/initCGALPlugin.cpp:24:
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In member function ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar*, Index, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index, RhsScalar*)’:
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  574 |         if(nr==4) traits.initAcc(C3);
      |         ^~
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:575:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  575 |                   traits.initAcc(C4);
      |                   ^~~~~~
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  946 |         if(nr==4) R3 = ploadu<ResPacket>(r3);
      |         ^~
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:948:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  948 |                   traits.acc(C0, alphav, R0);
      |                   ^~~~~~
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  951 |         if(nr==4) traits.acc(C3, alphav, R3);
      |         ^~
/home/owen/Softwares/sofa/src/SofaKernel/extlibs/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h:953:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  953 |                   pstoreu(r0, R0);
      |                   ^~~~~~~
In file included from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src/sofa/core/BaseMapping.h:27,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src/sofa/core/Mapping.h:25,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/../SofaSimulationCore/src/sofa/simulation/Node.h:51,
                 from /home/owen/Softwares/sofa/src/SofaKernel/modules/SofaHelper/../SofaSimulationCore/src/sofa/simulation/Simulation.h:25,
                 from /home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/MeshGenerationFromPolyhedron.h:39,
                 from /home/owen/Softwares/sofa/src/applications/plugins/CGALPlugin/initCGALPlugin.cpp:24:
/home/owen/Softwares/sofa/src/SofaKernel/modules/SofaCore/src/sofa/core/ConstraintParams.h: In member function ‘sofa::core::ConstraintParams& sofa::core::ConstraintParams::setX(sofa::core::ConstMultiVecCoordId)’:

...
ninja: build stopped: subcommand failed.

I am using gcc 9.3.0 and ninja to build SOFA. I wanted to use clang but on cmake, an error says “/usr/bin/clang++” is not able to compile a simple test program. Don’t know if it is related to the problem I am having…

This error really frustrates me! Please send help!

Kind regards,
Owen

[jnbrunet]

Hi Owen,

I’m not seeing any error message in your compilation output, only warnings. Did you truncate it?

JN

[Owen]

Hi JN,

Thank you for your reply.

Yes, the full output seems a bit too long. I just redirected it to a text file. Please find the file in the link: https://drive.google.com/open?id=1sfmqP_7E-r6_ziejZGYV-lICtGFjVBaY

Many thanks,
Owen

[jnbrunet]

Hi Owen,

Looks like the CGAL plugin is compiling with the c++11 standard, whereas the version of CGAL on ubuntu 20.04 (CGAL v5.0) is using c++14 features.

I’m guessing you are using the last stable version of SOFA (19.12)? This version set the c++ standard to c++11. This has changed in the development version, the next stable release of SOFA will be using c++17.

Meanwhile, you could:

1. Install an older version of CGAL (you can look on the CGAL website to learn how to get the source code and build/install it)

2. Or, you can manually specify your compiler to use the c++14 standard by editing the file sofa/applications/plugins/CGALPlugin/CMakeLists.txt, and anywhere after the add_library(${PROJECT_NAME} ...) (line 94 on the v19.12 source code), add the following :

target_compile_features(${PROJECT_NAME} PUBLIC cxx_std_14)

JN

[Owen]

Hi JN,

I tried the first suggestion and it works! You have really made my day. Thanks a million!

Best,
Owen

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