yade-dev team mailing list archive

["Vasileios Angelidakis (PGR)" <V.Angelidakis2@xxxxxxxxxxxxxxx>]

Hi all,


I just upgraded to Ubuntu 18.04 (which in retrospect doesn't feel like a good idea) and I have some difficulty building YADE from source. I cite below 1. the errors I get during configuring the build files and then 2. the errors I get when I try to compile them. Has anyone experienced similar problems? I would appreciate any advice on this.


Many thanks,


Vasileios


  *   1. Configuration of the compilation files

b7063391@sage17-drum008:~/myYade/newBuild_21_Jan_19$ cd /home/b7063391/myYade/newBuild_21_Jan_19/build
b7063391@sage17-drum008:~/myYade/newBuild_21_Jan_19/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/b7063391/myYade/newBuild_21_Jan_19/install /home/b7063391/myYade/newBuild_21_Jan_19/trunk
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- 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 "2.7.15")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
CMake Warning at /usr/share/cmake-3.10/Modules/FindQt4.cmake:620 (message):
  /usr/bin/qmake-qt4 reported QT_INSTALL_LIBS as "/usr/lib/x86_64-linux-gnu"
  but QtCore could not be found there.  Qt is NOT installed correctly for the
  target build environment.
Call Stack (most recent call first):
  CMakeLists.txt:39 (INCLUDE)


-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Version is set to 2019-01-04.git-f5aa5f7
-- 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 "1.13.3" /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: 1.65.1
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   chrono
--   atomic
--   Boost_VERSION: 106501
--   Boost_LIB_VERSION: 1_65_1
--   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/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libpthread.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 "2.7.15rc1")
-- Found Eigen3, version: 3.3.4
-- 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 5.1.2 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/b7063391/myYade/newBuild_21_Jan_19/install
-- Suffix is set to -2019-01-04.git-f5aa5f7
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/b7063391/myYade/newBuild_21_Jan_19/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 and <8 is found
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW LINSOLV TWOPHASEFLOW GL2PS LBMFLOW
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY THERMAL PROFILING PotentialParticles PotentialBlocks
-- Optimized build
-- ===========================================================
-- Configuring done
CMake Error: AUTOMOC: Qt4::moc target not found (WeightedAverage2d)
CMake Error: AUTOMOC: Qt4::moc target not found (_polyhedra_utils)
CMake Error: AUTOMOC: Qt4::moc target not found (_packObb)
-- Generating done
-- Build files have been written to: /home/b7063391/myYade/newBuild_21_Jan_19/build


  *   2. Compilation

b7063391@sage17-drum008:~/myYade/newBuild_21_Jan_19/build$ make -j4
Scanning dependencies of target _GLViewer_autogen
Scanning dependencies of target _packObb_autogen
Scanning dependencies of target WeightedAverage2d_autogen
Scanning dependencies of target _polyhedra_utils_autogen
[  0%] Automatic MOC for target WeightedAverage2d
[  0%] Automatic MOC for target _GLViewer
[  0%] Automatic MOC for target _packObb
[  0%] Automatic MOC for target _polyhedra_utils
[  0%] Built target WeightedAverage2d_autogen
[  0%] Built target _packObb_autogen
Scanning dependencies of target _packObb
Scanning dependencies of target WeightedAverage2d
[  0%] Built target _polyhedra_utils_autogen
make[2]: *** No rule to make target 'py/_packObb_autogen/mocs_compilation.cpp', needed by 'py/CMakeFiles/_packObb.dir/_packObb_autogen/mocs_compilation.cpp.o'. Stop.
make[2]: *** Waiting for unfinished jobs....
Scanning dependencies of target _polyhedra_utils
make[2]: *** No rule to make target 'py/WeightedAverage2d_autogen/mocs_compilation.cpp', needed by 'py/CMakeFiles/WeightedAverage2d.dir/WeightedAverage2d_autogen/mocs_compilation.cpp.o'. Stop.
make[2]: *** Waiting for unfinished jobs....
[  1%] Building CXX object py/CMakeFiles/_packObb.dir/pack/_packObb.cpp.o
[  1%] Building CXX object py/CMakeFiles/WeightedAverage2d.dir/WeightedAverage2d.cpp.o
make[2]: *** No rule to make target 'py/_polyhedra_utils_autogen/mocs_compilation.cpp', needed by 'py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils_autogen/mocs_compilation.cpp.o'. Stop.
make[2]: *** Waiting for unfinished jobs....
[  1%] Built target _GLViewer_autogen
Scanning dependencies of target _GLViewer
[  2%] Building CXX object py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o
[  3%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/GLViewer.cpp.o
CMakeFiles/Makefile2:701: recipe for target 'py/CMakeFiles/_packObb.dir/all' failed
make[1]: *** [py/CMakeFiles/_packObb.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  3%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/_GLViewer.cpp.o
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /home/b7063391/myYade/newBuild_21_Jan_19/trunk/py/_polyhedra_utils.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 " \
  ^~~~~~~
CMakeFiles/Makefile2:510: recipe for target 'py/CMakeFiles/WeightedAverage2d.dir/all' failed
make[1]: *** [py/CMakeFiles/WeightedAverage2d.dir/all] Error 2
[  4%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/OpenGLManager.cpp.o
/home/b7063391/myYade/newBuild_21_Jan_19/trunk/gui/qt5/GLViewer.cpp: In member function ‘virtual void GLViewer::keyPressEvent(QKeyEvent*)’:
/home/b7063391/myYade/newBuild_21_Jan_19/trunk/gui/qt5/GLViewer.cpp:252:36: warning: enum constant in boolean context [-Wint-in-bool-context]
    bool alt=(e->modifiers() && Qt::ShiftModifier);
                                    ^~~~~~~~~~~~~
[  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_autogen/mocs_compilation.cpp.o
CMakeFiles/Makefile2:547: recipe for target 'py/CMakeFiles/_polyhedra_utils.dir/all' failed
make[1]: *** [py/CMakeFiles/_polyhedra_utils.dir/all] Error 2
[  6%] Linking CXX shared library lib/x86_64-linux-gnu/_GLViewer.so
[  6%] Built target _GLViewer
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
b7063391@sage17-drum008:~/myYade/newBuild_21_Jan_19/build$