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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,
OwenHi Owen,
I’m not seeing any error message in your compilation output, only warnings. Did you truncate it?
JN
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,
OwenHi 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 theadd_library(${PROJECT_NAME} ...)(line 94 on the v19.12 source code), add the following :target_compile_features(${PROJECT_NAME} PUBLIC cxx_std_14)JN
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