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[Question #631403]: 'make' error during compilation

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: hjz <question631403@xxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 05 May 2017 15:57:52 -0000
Reply-to: question631403@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
New question #631403 on Yade:
https://answers.launchpad.net/yade/+question/631403

Hello everybody,

      I am installing “Yade 2017.01a” by compiling source code in ubuntu 14.04 (64bit). It reports errors when I execute 'make'. All the prerequisites have been installed.


Process of cmake：
hjz@hjz-System-Product-Name:~/myyade/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/hjz/myyade/install /home/hjz/myyade/trunk-2017.01
-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.6") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Version is set to 2017.01a
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so  
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/libgl2ps.so  
-- Found CGAL: /usr/include/CGAL, /usr/lib/libCGAL.so
-- Found NumPy: version "1.8.2" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include  
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   Boost_VERSION: 105400
--   Boost_LIB_VERSION: 1_54
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libpthread.so
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") 
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.6") 
-- Found Eigen3, version: 3.3.3
-- Disable vectorization
-- Found VTK
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so  
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer  
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu  
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found Cholmod: /usr/lib/libcholmod.so  
-- Found OpenBlas: /usr/lib/libopenblas.so  
-- Found Metis: /usr/include/metis  
-- Found Cholmod
-- Found OpenBlas
-- Found Metis
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
Yade will be installed to /home/hjz/myyade/install
-- Suffix is set to -2017.01a
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/hjz/myyade/install
-- Found gts: /usr/lib/python2.7/dist-packages/gts  
-- Use system gts version
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so  
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc  
-- VTK version >5 is found
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW LINSOLV GL2PS LBMFLOW
-- Disabled features: SPH LIQMIGRATION MASK_ARBITRARY PROFILING PotentialParticles PotentialBlocks
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hjz/myyade/build

Process of make：
hjz@hjz-System-Product-Name:~/myyade/build$ make
Scanning dependencies of target yade_automoc
[  1%] Automoc for target yade
[  1%] Built target yade_automoc
Scanning dependencies of target _GLViewer_automoc
[  2%] Automoc for target _GLViewer
Generating moc_GLViewer.cpp
Generating moc_OpenGLManager.cpp
[  2%] Built target _GLViewer_automoc
Scanning dependencies of target _GLViewer
[  3%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/GLViewer.cpp.o
[  3%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/_GLViewer.cpp.o
[  4%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/OpenGLManager.cpp.o
[  4%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/GLViewerDisplay.cpp.o
[  5%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/GLViewerMouse.cpp.o
[  5%] Building CXX object gui/CMakeFiles/_GLViewer.dir/_GLViewer_automoc.cpp.o
Linking CXX shared library lib/x86_64-linux-gnu/_GLViewer.so
[  5%] Built target _GLViewer
Scanning dependencies of target yade
[  6%] Building CXX object CMakeFiles/yade.dir/core/BodyContainer.cpp.o
[  6%] Building CXX object CMakeFiles/yade.dir/core/Material.cpp.o
[  7%] Building CXX object CMakeFiles/yade.dir/core/Cell.cpp.o
[  7%] Building CXX object CMakeFiles/yade.dir/core/Body.cpp.o
[  8%] Building CXX object CMakeFiles/yade.dir/core/ThreadRunner.cpp.o
[  8%] Building CXX object CMakeFiles/yade.dir/core/corePlugins.cpp.o
[  9%] Building CXX object CMakeFiles/yade.dir/core/State.cpp.o
[  9%] Building CXX object CMakeFiles/yade.dir/core/FileGenerator.cpp.o
[ 10%] Building CXX object CMakeFiles/yade.dir/core/ThreadWorker.cpp.o
[ 10%] Building CXX object CMakeFiles/yade.dir/core/ForceContainerParallel.cpp.o
[ 11%] Building CXX object CMakeFiles/yade.dir/core/Interaction.cpp.o
[ 11%] Building CXX object CMakeFiles/yade.dir/core/Omega.cpp.o
[ 12%] Building CXX object CMakeFiles/yade.dir/core/Scene.cpp.o
[ 13%] Building CXX object CMakeFiles/yade.dir/core/SimulationFlow.cpp.o
[ 13%] Building CXX object CMakeFiles/yade.dir/core/Clump.cpp.o
[ 14%] Building CXX object CMakeFiles/yade.dir/core/InteractionContainer.cpp.o
[ 14%] Building CXX object CMakeFiles/yade.dir/core/ForceContainerSerial.cpp.o
[ 15%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/UnsaturatedEngine.cpp.o
[ 15%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/PeriodicFlowEngine.cpp.o
[ 16%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/FlowEngine.cpp.o
[ 16%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/SoluteFlowEngine.cpp.o
[ 17%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/DFNFlow.cpp.o
[ 17%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/TwoPhaseFlowEngine.cpp.o
[ 18%] Building CXX object CMakeFiles/yade.dir/pkg/pfv/DummyFlowEngine.cpp.o
[ 18%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ig2_PP_PP_ScGeom.cpp.o
[ 19%] Building CXX object CMakeFiles/yade.dir/pkg/dem/RungeKuttaCashKarp54Integrator.cpp.o
[ 19%] Building CXX object CMakeFiles/yade.dir/pkg/dem/GlobalStiffnessTimeStepper.cpp.o
[ 20%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialStressController.cpp.o
[ 20%] Building CXX object CMakeFiles/yade.dir/pkg/dem/MicroMacroAnalyser.cpp.o
[ 21%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ig2_PB_PB_ScGeom.cpp.o
[ 21%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PotentialBlock.cpp.o
[ 22%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ConcretePM.cpp.o
[ 22%] Building CXX object CMakeFiles/yade.dir/pkg/dem/MortarMat.cpp.o
[ 23%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryPhys1.cpp.o
[ 23%] Building CXX object CMakeFiles/yade.dir/pkg/dem/NewtonIntegrator.cpp.o
[ 24%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CohesiveFrictionalContactLaw.cpp.o
[ 24%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TesselationWrapper.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/hjz/myyade/trunk-2017.01/lib/pyutil/numpy_boost.hpp:40,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/TesselationWrapper.cpp:15:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/hjz/myyade/trunk-2017.01/lib/pyutil/numpy_boost.hpp:40,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/TesselationWrapper.cpp:15:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
[ 25%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o
[ 26%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PeriIsoCompressor.cpp.o
[ 26%] Building CXX object CMakeFiles/yade.dir/pkg/dem/UniaxialStrainer.cpp.o
[ 27%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FlatGridCollider.cpp.o
[ 27%] Building CXX object CMakeFiles/yade.dir/pkg/dem/RockLiningGlobal.cpp.o
[ 28%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Shop_02.cpp.o
[ 28%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ip2_ElastMat.cpp.o
[ 29%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Disp2DPropLoadEngine.cpp.o
[ 29%] Building CXX object CMakeFiles/yade.dir/pkg/dem/WirePM.cpp.o
[ 30%] Building CXX object CMakeFiles/yade.dir/pkg/dem/GeneralIntegratorInsertionSortCollider.cpp.o
[ 30%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Tetra.cpp.o
[ 31%] Building CXX object CMakeFiles/yade.dir/pkg/dem/UnbalancedForceCallbacks.cpp.o
[ 31%] Building CXX object CMakeFiles/yade.dir/pkg/dem/DomainLimiter.cpp.o
[ 32%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PotentialBlock2AABB.cpp.o
[ 32%] Building CXX object CMakeFiles/yade.dir/pkg/dem/RockBolt.cpp.o
[ 33%] Building CXX object CMakeFiles/yade.dir/pkg/dem/KinemSimpleShearBox.cpp.o
[ 33%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryTriaxialTest.cpp.o
[ 34%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Integrator.cpp.o
[ 34%] Building CXX object CMakeFiles/yade.dir/pkg/dem/LudingPM.cpp.o
[ 35%] Building CXX object CMakeFiles/yade.dir/pkg/dem/JointedCohesiveFrictionalPM.cpp.o
[ 35%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CapillaryStressRecorder.cpp.o
[ 36%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialCompressionEngine.cpp.o
[ 36%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ig2_Box_Sphere_ScGeom.cpp.o
[ 37%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp.o
[ 38%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Ig2_Sphere_Sphere_ScGeom.cpp.o
[ 38%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity1.cpp.o
[ 39%] Building CXX object CMakeFiles/yade.dir/pkg/dem/FrictPhys.cpp.o
[ 39%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ForceTorqueRecorder.cpp.o
[ 40%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ViscoelasticPM.cpp.o
[ 40%] Building CXX object CMakeFiles/yade.dir/pkg/dem/CohesiveTriaxialTest.cpp.o
[ 41%] Building CXX object CMakeFiles/yade.dir/pkg/dem/ScGeom.cpp.o
[ 41%] Building CXX object CMakeFiles/yade.dir/pkg/dem/VTKRecorder.cpp.o
In file included from /usr/include/vtk-6.0/vtkTriangle.h:26:0,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:16:
/usr/include/vtk-6.0/vtkMath.h: In static member function ‘static int vtkMath::IsInf(double)’:
/usr/include/vtk-6.0/vtkMath.h:1249:18: error: call of overloaded ‘isinf(double&)’ is ambiguous
   return (isinf(x) != 0); // Force conversion to bool
                  ^
/usr/include/vtk-6.0/vtkMath.h:1249:18: note: candidates are:
In file included from /usr/include/math.h:69:0,
                 from /usr/include/c++/4.8/cmath:44,
                 from /home/hjz/myyade/trunk-2017.01/lib/base/Math.hpp:12,
                 from /home/hjz/myyade/trunk-2017.01/lib/serialization/Serializable.hpp:15,
                 from /home/hjz/myyade/trunk-2017.01/core/Engine.hpp:13,
                 from /home/hjz/myyade/trunk-2017.01/core/GlobalEngine.hpp:11,
                 from /home/hjz/myyade/trunk-2017.01/pkg/common/PeriodicEngines.hpp:5,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.hpp:2,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:3:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:201:12: note: int isinf(double)
 __MATHDECL_1 (int,isinf,, (_Mdouble_ __value)) __attribute__ ((__const__));
            ^
In file included from /home/hjz/myyade/trunk-2017.01/lib/base/Math.hpp:12:0,
                 from /home/hjz/myyade/trunk-2017.01/lib/serialization/Serializable.hpp:15,
                 from /home/hjz/myyade/trunk-2017.01/core/Engine.hpp:13,
                 from /home/hjz/myyade/trunk-2017.01/core/GlobalEngine.hpp:11,
                 from /home/hjz/myyade/trunk-2017.01/pkg/common/PeriodicEngines.hpp:5,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.hpp:2,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:3:
/usr/include/c++/4.8/cmath:608:3: note: constexpr bool std::isinf(long double)
   isinf(long double __x)
   ^
/usr/include/c++/4.8/cmath:604:3: note: constexpr bool std::isinf(double)
   isinf(double __x)
   ^
/usr/include/c++/4.8/cmath:600:3: note: constexpr bool std::isinf(float)
   isinf(float __x)
   ^
In file included from /usr/include/vtk-6.0/vtkTriangle.h:26:0,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:16:
/usr/include/vtk-6.0/vtkMath.h: In static member function ‘static int vtkMath::IsNan(double)’:
/usr/include/vtk-6.0/vtkMath.h:1259:18: error: call of overloaded ‘isnan(double&)’ is ambiguous
   return (isnan(x) != 0); // Force conversion to bool
                  ^
/usr/include/vtk-6.0/vtkMath.h:1259:18: note: candidates are:
In file included from /usr/include/math.h:69:0,
                 from /usr/include/c++/4.8/cmath:44,
                 from /home/hjz/myyade/trunk-2017.01/lib/base/Math.hpp:12,
                 from /home/hjz/myyade/trunk-2017.01/lib/serialization/Serializable.hpp:15,
                 from /home/hjz/myyade/trunk-2017.01/core/Engine.hpp:13,
                 from /home/hjz/myyade/trunk-2017.01/core/GlobalEngine.hpp:11,
                 from /home/hjz/myyade/trunk-2017.01/pkg/common/PeriodicEngines.hpp:5,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.hpp:2,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:3:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:234:12: note: int isnan(double)
 __MATHDECL_1 (int,isnan,, (_Mdouble_ __value)) __attribute__ ((__const__));
            ^
In file included from /home/hjz/myyade/trunk-2017.01/lib/base/Math.hpp:12:0,
                 from /home/hjz/myyade/trunk-2017.01/lib/serialization/Serializable.hpp:15,
                 from /home/hjz/myyade/trunk-2017.01/core/Engine.hpp:13,
                 from /home/hjz/myyade/trunk-2017.01/core/GlobalEngine.hpp:11,
                 from /home/hjz/myyade/trunk-2017.01/pkg/common/PeriodicEngines.hpp:5,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.hpp:2,
                 from /home/hjz/myyade/trunk-2017.01/pkg/dem/VTKRecorder.cpp:3:
/usr/include/c++/4.8/cmath:626:3: note: constexpr bool std::isnan(long double)
   isnan(long double __x)
   ^
/usr/include/c++/4.8/cmath:622:3: note: constexpr bool std::isnan(double)
   isnan(double __x)
   ^
/usr/include/c++/4.8/cmath:618:3: note: constexpr bool std::isnan(float)
   isnan(float __x)
   ^
make[2]: *** [CMakeFiles/yade.dir/pkg/dem/VTKRecorder.cpp.o] Error 1
make[1]: *** [CMakeFiles/yade.dir/all] Error 2
make: *** [all] Error 2

sincerely,
hjz



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