yade installation error

Hello,

Which Linux distribution are you using? There are a few causes and solutions to this undefined symbol problem [1][2][3][4]. Maybe [1] is most relevant to you.

Please post your cmake output so we can see if you are linking to the proper libraries.

Also, what happens when you try running 'sudo yade-2017-12-21.git-d6cfc7' ?

Cheers,

Robert

[1]https://answers.launchpad.net/yade/+question/247246
[2]https://answers.launchpad.net/yade/+question/293500
[3]https://answers.launchpad.net/yade/+question/662104
[4]https://answers.launchpad.net/yade/+question/281177

Hi Robert,

I use Ubuntu 16.04 and I get this when we first run cmake as follows:

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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 "2.7.12")
-- 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 (found version "4.8.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Version is set to 2017-12-21.git-d6cfc7f
-- 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, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- Found NumPy: version "1.11.0" /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
-- GCC Version >= 4.9. Adding -fstack-protector-strong
CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725 (message):
  Imported targets not available for Boost version 106501
Call Stack (most recent call first):
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:763 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:94 (FIND_PACKAGE)

-- 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
-- Boost_VERSION: 106501
-- Boost_LIB_VERSION: 1_65_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/libboost_python.so/usr/lib/libboost_thread.so/usr/lib/libboost_filesystem.so/usr/lib/libboost_iostreams.so/usr/lib/libboost_regex.so/usr/lib/libboost_serialization.so/usr/lib/libboost_system.so/usr/lib/libboost_date_time.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 "1.2.8")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.12")
-- Found Eigen3, version: 3.2.92
-- 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-6.2/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-6.2/VTKTargets.cmake"
but not all the files it references.

-- 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/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas: /usr/lib/libopenblas.so
-- Could NOT find Metis (missing: METIS_INCLUDE_DIR METIS_LIBRARY)
-- Missing dependency for LINSOLV, disabled
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
Yade will be installed to /home/ozge/UTILS/yade/install
-- Suffix is set to -2017-12-21.git-d6cfc7f
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/ozge/UTILS/yade/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 GL2PS LBMFLOW
-- Disabled features: LINSOLV SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING PotentialParticles PotentialBlocks
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ozge/UTILS/yade/build

Earlier when I am able to compile it I have also tested running "sudo yade-2017-12-21.git-d6cfc7" but it gave the similar error.

thank you for your kind interest

Özge

It seems you are missing quite a few boost dependencies. Did you solve this?