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[Bug 1322274] [NEW] yade -DDEBUG=True run error

To: yade-dev@xxxxxxxxxxxxxxxxxxx
From: Chao Yuan <chaoyuan2012@xxxxxxxxx>
Date: Thu, 22 May 2014 17:11:02 -0000
Reply-to: Bug 1322274 <1322274@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
Public bug reported:

I install yade from trunk with -DDEBUG=ON (my OS: Kubuntu 12.04). It can
make install successfully. But when running it, it complains:

cyuan@dt-med006:~/temp$ ../yade/bin/yade-chaoDebug
Welcome to Yade 2014-05-19.git-fd1a0bc 
Traceback (most recent call last):
  File "../yade/bin/yade-chaoDebug", line 125, in <module>
    import yade
  File "/home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chaoDebug/py/yade/__init__.py", line 65, in <module>
    import boot
ImportError: /home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chaoDebug/libyade.so: undefined symbol: _ZNK5boost9gregorian10greg_month15as_short_stringEv

Cmake output is:

cmake -DINSTALL_PREFIX=/home/3S-LAB/cyuan/yade/ /home/3S-LAB/cyuan/trunk
-DSUFFIX="-chaoDebug" -DCMAKE_CXX_FLAGS="-DFLOW_ENGINE"
-DENABLE_LINSOLV=OFF -DDEBUG=ON

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- 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 PythonLibs: /usr/lib/libpython2.7.so
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
-- 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 "4.8.1")
-- Version is set to 2014-05-19.git-fd1a0bc
-- 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 "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include
-- Boost version: 1.46.1
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
--   Boost_VERSION: 104601
--   Boost_LIB_VERSION: 1_46_1
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: /usr/lib/libboost_python.so/usr/lib/libboost_thread-mt.sopthread/usr/lib/libboost_filesystem-mt.so/usr/lib/libboost_iostreams-mt.so/usr/lib/libboost_regex-mt.so/usr/lib/libboost_serialization-mt.so/usr/lib/libboost_system-mt.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so
-- 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 "1.2.3.4")
-- Found Eigen3
-- Boost Odeint can be enabled, only if Boost>=1.53 is used
-- 1
-- 46
-- 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 files HAVE_GLIB_GREGEX_H
-- Looking for include files HAVE_GLIB_GREGEX_H - found
-- Found GTS
-- Found Qt4: /usr/bin/qmake (found version "4.8.1")
-- Found QGLViewer: /usr/lib/x86_64-linux-gnu/libqglviewer-qt4.so
-- Found GUI-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found GL2PS
Yade will be installed to /home/3S-LAB/cyuan/yade
-- Suffix is set to -chaoDebug
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/3S-LAB/cyuan/yade
-- Could NOT find gts (missing:  PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
-- Could NOT find minieigen (missing:  PY_minieigen)
-- Use embedded version of minieigen. Please, consider installing the corresponding package
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc
-- ===========================================================
-- Yade configured with following features: Eigen3 VTK OpenMP GTS GUI CGAL PFVflow GL2PS
-- Disabled features: Odeint LinSolv SPH LIQMIGRATION LBMFLOW
-- Debug build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/3S-LAB/cyuan/trunkVersions/debug/build

** Affects: yade
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1322274

Title:
  yade -DDEBUG=True run error

Status in Yet Another Dynamic Engine:
  New

Bug description:
  I install yade from trunk with -DDEBUG=ON (my OS: Kubuntu 12.04). It
  can make install successfully. But when running it, it complains:

  cyuan@dt-med006:~/temp$ ../yade/bin/yade-chaoDebug
  Welcome to Yade 2014-05-19.git-fd1a0bc 
  Traceback (most recent call last):
    File "../yade/bin/yade-chaoDebug", line 125, in <module>
      import yade
    File "/home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chaoDebug/py/yade/__init__.py", line 65, in <module>
      import boot
  ImportError: /home/3S-LAB/cyuan/yade/lib/x86_64-linux-gnu/yade-chaoDebug/libyade.so: undefined symbol: _ZNK5boost9gregorian10greg_month15as_short_stringEv

  Cmake output is:

  cmake -DINSTALL_PREFIX=/home/3S-LAB/cyuan/yade/ /home/3S-
  LAB/cyuan/trunk -DSUFFIX="-chaoDebug"
  -DCMAKE_CXX_FLAGS="-DFLOW_ENGINE" -DENABLE_LINSOLV=OFF -DDEBUG=ON

  -- The C compiler identification is GNU
  -- The CXX compiler identification is GNU
  -- Check for working C compiler: /usr/bin/gcc
  -- Check for working C compiler: /usr/bin/gcc -- 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 PythonLibs: /usr/lib/libpython2.7.so
  -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
  -- 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 "4.8.1")
  -- Version is set to 2014-05-19.git-fd1a0bc
  -- 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 "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
  -- Found Loki: /usr/include
  -- Boost version: 1.46.1
  -- Found the following Boost libraries:
  -- python
  -- thread
  -- filesystem
  -- iostreams
  -- regex
  -- serialization
  -- system
  --   Boost_VERSION: 104601
  --   Boost_LIB_VERSION: 1_46_1
  --   Boost_INCLUDE_DIRS: /usr/include
  --   Boost_LIBRARIES: /usr/lib/libboost_python.so/usr/lib/libboost_thread-mt.sopthread/usr/lib/libboost_filesystem-mt.so/usr/lib/libboost_iostreams-mt.so/usr/lib/libboost_regex-mt.so/usr/lib/libboost_serialization-mt.so/usr/lib/libboost_system-mt.so
  -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
  -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so
  -- 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 "1.2.3.4")
  -- Found Eigen3
  -- Boost Odeint can be enabled, only if Boost>=1.53 is used
  -- 1
  -- 46
  -- 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 files HAVE_GLIB_GREGEX_H
  -- Looking for include files HAVE_GLIB_GREGEX_H - found
  -- Found GTS
  -- Found Qt4: /usr/bin/qmake (found version "4.8.1")
  -- Found QGLViewer: /usr/lib/x86_64-linux-gnu/libqglviewer-qt4.so
  -- Found GUI-LIBS
  -- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
  -- Found GMP: /usr/include
  -- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
  -- Found CGAL
  -- Found GL2PS
  Yade will be installed to /home/3S-LAB/cyuan/yade
  -- Suffix is set to -chaoDebug
  -- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
  -- runtimePREFIX is set to /home/3S-LAB/cyuan/yade
  -- Could NOT find gts (missing:  PY_gts)
  -- Use embedded version of gts. Please, consider installing the corresponding package
  -- Could NOT find minieigen (missing:  PY_minieigen)
  -- Use embedded version of minieigen. Please, consider installing the corresponding package
  -- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc
  -- ===========================================================
  -- Yade configured with following features: Eigen3 VTK OpenMP GTS GUI CGAL PFVflow GL2PS
  -- Disabled features: Odeint LinSolv SPH LIQMIGRATION LBMFLOW
  -- Debug build
  -- ===========================================================
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /home/3S-LAB/cyuan/trunkVersions/debug/build

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Follow ups

[Bug 1322274] Re: yade -DDEBUG=True run error
From: Anton Gladky, 2014-05-23
[Bug 1322274] Re: yade -DDEBUG=True run error
From: Bruno Chareyre, 2014-05-23
[Bug 1322274] Re: yade -DDEBUG=True run error
From: Chao Yuan, 2014-05-23
[Bug 1322274] Re: yade -DDEBUG=True run error
From: Anton Gladky, 2014-05-23
[Bug 1322274] [NEW] yade -DDEBUG=True run error
From: Chao Yuan, 2014-05-22
References

[Bug 1322274] [NEW] yade -DDEBUG=True run error
From: Chao Yuan, 2014-05-22