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[Question #688588]: Compilation error

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Lingran Zhang <question688588@xxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 07 Feb 2020 18:08:42 -0000
Reply-to: question688588@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
New question #688588 on Yade:
https://answers.launchpad.net/yade/+question/688588

Hi all,

I got this error message at 67% Yade compilation on Debian 10. The code was modified from trunk sometimes ago, but earlier the same code was able to be installed on Ubuntu 16.04.

Here is the error:

[ 65%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialCompressionEngine.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/lib/pyutil/numpy_boost.hpp:40,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/pkg/dem/TesselationWrapper.cpp:15:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
[ 66%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialStateRecorder.cpp.o
[ 66%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialStressController.cpp.o
In file included from /home/mohammay/Documents/yadeInstall/trunkModify/lib/triangulation/Tesselation.h:202,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/pkg/dem/TesselationWrapper.hpp:15,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/pkg/dem/TesselationWrapper.cpp:12:
/home/mohammay/Documents/yadeInstall/trunkModify/lib/triangulation/Tesselation.ipp: In instantiation of ‘CGT::_Tesselation<TT>::VertexHandle CGT::_Tesselation<TT>::move(CGT::Real, CGT::Real, CGT::Real, CGT::Real, unsigned int) [with TT = CGT::TriangulationTypes<CGT::SimpleVertexInfo, CGT::SimpleCellInfo>; CGT::_Tesselation<TT>::VertexHandle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, CGAL::Triangulation_vertex_base_with_info_3<CGT::SimpleVertexInfo, CGAL::Epick, CGAL::Regular_triangulation_vertex_base_3<CGAL::Epick, CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, CGAL::Triangulation_vertex_base_with_info_3<CGT::SimpleVertexInfo, CGAL::Epick, CGAL::Regular_triangulation_vertex_base_3<CGAL::Epick> >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_with_info_3<CGT::SimpleCellInfo, CGAL::Epick, CGAL::Regular_triangulation_cell_base_3<CGAL::Epick> >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Sequential_tag> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>; CGT::Real = double]’:
/home/mohammay/Documents/yadeInstall/trunkModify/pkg/dem/TesselationWrapper.cpp:186:28:   required from here
/home/mohammay/Documents/yadeInstall/trunkModify/lib/triangulation/Tesselation.ipp:78:12: error: ‘CGT::_Tesselation<CGT::TriangulationTypes<CGT::SimpleVertexInfo, CGT::SimpleCellInfo> >::RTriangulation’ {aka ‘class CGAL::Regular_triangulation_3<CGAL::Epick, CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, CGAL::Triangulation_vertex_base_with_info_3<CGT::SimpleVertexInfo, CGAL::Epick, CGAL::Regular_triangulation_vertex_base_3<CGAL::Epick> >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_with_info_3<CGT::SimpleCellInfo, CGAL::Epick, CGAL::Regular_triangulation_cell_base_3<CGAL::Epick> >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Sequential_tag>, CGAL::Default>’} has no member named ‘move_point’; did you mean ‘Bare_point’?
  Vh = Tri->move_point ( vertexHandles[id], Sphere ( Point ( x,y,z ),pow ( rad,2 ) ) );
       ~~~~~^~~~~~~~~~
       Bare_point
[ 67%] Building CXX object CMakeFiles/yade.dir/pkg/dem/TriaxialTest.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:21,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/lib/pyutil/numpy_boost.hpp:40,
                 from /home/mohammay/Documents/yadeInstall/trunkModify/pkg/dem/TesselationWrapper.cpp:15:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
make[2]: *** [CMakeFiles/yade.dir/build.make:1493: CMakeFiles/yade.dir/pkg/dem/TesselationWrapper.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:145: CMakeFiles/yade.dir/all] Error 2
make: *** [Makefile:130: all] Error 2




Here is the cmake information:

-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.16") 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
qmake: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/qmake': No such file or directory
-- Found unsuitable Qt version "" from NOTFOUND
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29") 
-- Version is set to Unknown
CMake Warning (dev) at /usr/share/cmake-3.13/Modules/FindOpenGL.cmake:270 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/lib/x86_64-linux-gnu/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/lib/x86_64-linux-gnu/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/lib/x86_64-linux-gnu/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  CMakeLists.txt:41 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so   
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so  
-- Found CGAL: /usr/include, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- Found NumPy: version "1.16.2" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include  
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.67.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   chrono
--   atomic
--   Boost_VERSION: 106700
--   Boost_LIB_VERSION: 1_67
--   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-lpthread/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/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so
-- Found Eigen3: /usr/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
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.16") 
-- Found Eigen3, version: 3.3.7
-- Disable vectorization
-- The imported target "vtkRenderingPythonTkWidgets" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtk" references the file
   "/usr/bin/vtk"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- 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  
-- USE QT5
-- 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
-- SuiteSparse version 5.4.0 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so  
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so  
-- Found Metis: /usr/include  
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
Yade will be installed to /home/mohammay/Documents/yadeInstall/install
-- Suffix is set to -Unknown
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/mohammay/Documents/yadeInstall/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 TWOPHASEFLOW LINSOLV GL2PS LBMFLOW
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING PotentialParticles PotentialBlocks
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/mohammay/Documents/yadeInstall/build


Any ideas what's wrong? is it related to VTK?

Thank you!

Lingran





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