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I have been trying to build molekel 5.2 from the source. I am getting linking errors at the final stage during building of the executable. Any ideas?
The installation is on a x86_64 with redhat enterprise linux 5. The error log and the contents of the CMakeCache.txt are below.
Thanks,
-Taner
-- error.log ----------------------------------------------------
[diramate@blue build]$ make
[ 1%] Generating moc_EventPositionTimeWidget.cxx
[ 2%] Generating moc_MainWindow.cxx
[ 3%] Generating moc_MoleculeRenderingStyleWidget.cxx
[ 4%] Generating moc_WorkspaceTreeWidget.cxx
[ 5%] Generating moc_MoleculeVibrationWidget.cxx
[ 6%] Generating moc_MoleculeTrajectoryWidget.cxx
[ 7%] Generating moc_MoleculeAnimationModeWidget.cxx
[ 8%] Generating moc_TimeStepWidget.cxx
[ 9%] Generating moc_MoleculeElDensSurfaceWidget.cxx
[ 10%] Generating moc_ImagePlaneProbeWidget.cxx
[ 11%] Generating moc_GridDataSurfaceWidget.cxx
[ 12%] Generating moc_SasWidget.cxx
[ 13%] Generating moc_SesWidget.cxx
[ 14%] Generating moc_ViewPropertiesWidget.cxx
[ 15%] Generating moc_ShaderWidget.cxx
[ 16%] Generating moc_MoleculeAnimationDialog.cxx
[ 17%] Generating moc_TimeStepDialog.cxx
[ 18%] Generating moc_ComputeElDensSurfaceDialog.cxx
[ 19%] Generating moc_ImagePlaneProbeDialog.cxx
[ 20%] Generating moc_GridDataSurfaceDialog.cxx
[ 21%] Generating moc_ExportAnimationDialog.cxx
[ 22%] Generating moc_SasDialog.cxx
[ 23%] Generating moc_SesDialog.cxx
[ 24%] Generating moc_ShadersDialog.cxx
[ 25%] Generating moc_EventFilter.cxx
[ 26%] Generating moc_EventPlayer.cxx
[ 27%] Generating moc_EventRecorderWidget.cxx
[ 28%] Generating moc_EventPlayerWidget.cxx
[ 29%] Generating moc_QGLSLShaderEditorWidget.cxx
Scanning dependencies of target Molekel
[ 29%] Building CXX object CMakeFiles/Molekel.dir/versioninfo.o
[ 30%] Building CXX object CMakeFiles/Molekel.dir/main.o
[ 31%] Building CXX object CMakeFiles/Molekel.dir/MainWindow.o
[ 32%] Building CXX object CMakeFiles/Molekel.dir/MolekelMolecule.o
[ 33%] Building CXX object CMakeFiles/Molekel.dir/MolekelData.o
[ 34%] Building CXX object CMakeFiles/Molekel.dir/old/molekeltypes.o
[ 35%] Building CXX object CMakeFiles/Molekel.dir/old/readgauss.o
[ 36%] Building CXX object CMakeFiles/Molekel.dir/old/readgamess.o
[ 37%] Building CXX object CMakeFiles/Molekel.dir/old/calcdens.o
[ 38%] Building CXX object CMakeFiles/Molekel.dir/old/utilities.o
[ 39%] Building CXX object CMakeFiles/Molekel.dir/old/readmolden.o
[ 40%] Building CXX object CMakeFiles/Molekel.dir/resources/icon.o
[ 41%] Building CXX object CMakeFiles/Molekel.dir/resources/atomsdata.o
[ 42%] Building CXX object CMakeFiles/Molekel.dir/resources/license.o
[ 43%] Building CXX object CMakeFiles/Molekel.dir/utility/CommandLine.o
[ 44%] Building CXX object CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o
[ 45%] Building CXX object CMakeFiles/Molekel.dir/utility/MolekelChemPDBImporter.o
[ 46%] Building CXX object CMakeFiles/Molekel.dir/utility/BabelToMOIV.o
[ 47%] Building CXX object CMakeFiles/Molekel.dir/utility/vtkMSMSReader.o
[ 48%] Building CXX object CMakeFiles/Molekel.dir/utility/System.o
[ 49%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o
[ 50%] Building CXX object CMakeFiles/Molekel.dir/utility/ElementTable.o
[ 51%] Building CXX object CMakeFiles/Molekel.dir/utility/MolekelToOpenBabel.o
[ 52%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMoldenFormat.o
[ 53%] Building CXX object CMakeFiles/Molekel.dir/utility/OBZmatrixFormat.o
[ 54%] Building CXX object CMakeFiles/Molekel.dir/utility/OBT41Format.o
[ 55%] Building CXX object CMakeFiles/Molekel.dir/utility/events/ObjectName.o
[ 56%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventPlayer.o
[ 57%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventRecorderWidget.o
[ 58%] Building CXX object CMakeFiles/Molekel.dir/utility/events/EventPlayerWidget.o
[ 59%] Building CXX object CMakeFiles/Molekel.dir/utility/vtkGLSLShaderActor.o
[ 60%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/Shaders.o
[ 61%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/ShaderParameters.o
[ 62%] Building CXX object CMakeFiles/Molekel.dir/utility/shaders/QGLSLShaderEditorWidget.o
[ 63%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeRenderingStyleWidget.o
[ 64%] Building CXX object CMakeFiles/Molekel.dir/widgets/WorkspaceTreeWidget.o
[ 65%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeVibrationWidget.o
[ 66%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeTrajectoryWidget.o
[ 67%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeAnimationModeWidget.o
[ 68%] Building CXX object CMakeFiles/Molekel.dir/widgets/TimeStepWidget.o
[ 69%] Building CXX object CMakeFiles/Molekel.dir/widgets/MoleculeElDensSurfaceWidget.o
[ 70%] Building CXX object CMakeFiles/Molekel.dir/widgets/ImagePlaneProbeWidget.o
[ 71%] Building CXX object CMakeFiles/Molekel.dir/widgets/GridDataSurfaceWidget.o
[ 72%] Building CXX object CMakeFiles/Molekel.dir/moc_MainWindow.o
[ 73%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeRenderingStyleWidget.o
[ 74%] Building CXX object CMakeFiles/Molekel.dir/moc_WorkspaceTreeWidget.o
[ 75%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeVibrationWidget.o
[ 76%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeTrajectoryWidget.o
[ 77%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeAnimationModeWidget.o
[ 78%] Building CXX object CMakeFiles/Molekel.dir/moc_TimeStepWidget.o
[ 79%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeElDensSurfaceWidget.o
[ 80%] Building CXX object CMakeFiles/Molekel.dir/moc_ImagePlaneProbeWidget.o
[ 81%] Building CXX object CMakeFiles/Molekel.dir/moc_GridDataSurfaceWidget.o
[ 82%] Building CXX object CMakeFiles/Molekel.dir/moc_SasWidget.o
[ 83%] Building CXX object CMakeFiles/Molekel.dir/moc_SesWidget.o
[ 84%] Building CXX object CMakeFiles/Molekel.dir/moc_ViewPropertiesWidget.o
[ 85%] Building CXX object CMakeFiles/Molekel.dir/moc_ShaderWidget.o
[ 86%] Building CXX object CMakeFiles/Molekel.dir/moc_MoleculeAnimationDialog.o
[ 87%] Building CXX object CMakeFiles/Molekel.dir/moc_TimeStepDialog.o
[ 88%] Building CXX object CMakeFiles/Molekel.dir/moc_ComputeElDensSurfaceDialog.o
[ 89%] Building CXX object CMakeFiles/Molekel.dir/moc_ImagePlaneProbeDialog.o
[ 90%] Building CXX object CMakeFiles/Molekel.dir/moc_GridDataSurfaceDialog.o
[ 91%] Building CXX object CMakeFiles/Molekel.dir/moc_ExportAnimationDialog.o
[ 92%] Building CXX object CMakeFiles/Molekel.dir/moc_SasDialog.o
[ 93%] Building CXX object CMakeFiles/Molekel.dir/moc_SesDialog.o
[ 94%] Building CXX object CMakeFiles/Molekel.dir/moc_ShadersDialog.o
[ 95%] Building CXX object CMakeFiles/Molekel.dir/moc_EventFilter.o
[ 96%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPlayer.o
[ 97%] Building CXX object CMakeFiles/Molekel.dir/moc_EventRecorderWidget.o
[ 98%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPlayerWidget.o
[ 99%] Building CXX object CMakeFiles/Molekel.dir/moc_QGLSLShaderEditorWidget.o
[100%] Building CXX object CMakeFiles/Molekel.dir/moc_EventPositionTimeWidget.o
Linking CXX executable dist/bin/Molekel
CMakeFiles/Molekel.dir/utility/System.o: In function `GetTemporaryFileName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
System.cpp:(.text+0x3ae): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat15WriteChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::WriteChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)':
OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat14ReadChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flMakeCurrentFont'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flDestroyFont'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flGetCurrentContext'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flGetCurrentFont'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flSetHint'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flCreateFont'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flCreateContext'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flGetBitmap'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flFreeBitmap'
/apps/molekel_related/OpenMOIV.src.1.0.3/libChemKit2.so: undefined reference to `flMakeCurrentContext'
collect2: ld returned 1 exit status
make[2]: *** [dist/bin/Molekel] Error 1
make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2
make: *** [all] Error 2
-- CMakeCache.txt ---------------------------------------------------------
# This is the CMakeCache file.
# For build in directory: /apps/molekel_src_5.2/build
# It was generated by CMake: /apps/molekel_related/cmake-2.4.6-Linux-i386/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
//Path to a program.
CMAKE_AR:FILEPATH=/usr/bin/ar
//For backwards compatibility, what version of CMake commands and
// syntax should this version of CMake allow.
CMAKE_BACKWARDS_COMPATIBILITY:STRING=2.4
//Choose the type of build, options are: None(CMAKE_CXX_FLAGS or
// CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.
//
CMAKE_BUILD_TYPE:STRING=
//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON
//CXX compiler.
CMAKE_CXX_COMPILER:FILEPATH=/usr/local/bin/g++
//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=-L /usr/local/lib64
//Flags used by the compiler during debug builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=-g
//Flags used by the compiler during release minsize builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds (/MD /Ob1 /Oi
// /Ot /Oy /Gs will produce slightly less optimized but smaller
// files).
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
//Flags used by the compiler during Release with Debug Info builds.
//
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CMAKE_C_COMPILER:FILEPATH=/usr/local/bin/gcc
//Flags for C compiler.
CMAKE_C_FLAGS:STRING=' '
//Flags used by the compiler during debug builds.
CMAKE_C_FLAGS_DEBUG:STRING=-g
//Flags used by the compiler during release minsize builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG
//Flags used by the compiler during release builds (/MD /Ob1 /Oi
// /Ot /Oy /Gs will produce slightly less optimized but smaller
// files).
CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
//Flags used by the compiler during Release with Debug Info builds.
//
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g
//Flags used by the linker.
CMAKE_EXE_LINKER_FLAGS:STRING=
//Flags used by the linker during debug builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
//
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Install path prefix, prepended onto install directories.
CMAKE_INSTALL_PREFIX:PATH=/usr/local
//Path to a program.
CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/gmake
//Flags used by the linker during the creation of modules.
CMAKE_MODULE_LINKER_FLAGS:STRING=
//Flags used by the linker during debug builds.
CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
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//Flags used by the linker during Release with Debug Info builds.
//
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//Path to a program.
CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib
//Flags used by the linker during the creation of dll's.
CMAKE_SHARED_LINKER_FLAGS:STRING=
//Flags used by the linker during debug builds.
CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=
//Flags used by the linker during release minsize builds.
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=
//Flags used by the linker during release builds.
CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=
//Flags used by the linker during Release with Debug Info builds.
//
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=
//If set, runtime paths are not added when using shared libraries.
//
CMAKE_SKIP_RPATH:BOOL=NO
//If true, cmake will use relative paths in makefiles and projects.
//
CMAKE_USE_RELATIVE_PATHS:BOOL=OFF
//If this value is on, makefiles will be generated without the
// .SILENT directive, and all commands will be echoed to the console
// during the make. This is useful for debugging only. With Visual
// Studio IDE projects all commands are done without /nologo.
CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE
//Single output directory for building all executables.
EXECUTABLE_OUTPUT_PATH:PATH=
//GLEW include dir
GLEW_INCLUDE_DIR:PATH=/apps/glew/include
//GLEW link dir
GLEW_LINK_DIR:PATH=/apps/glew/lib
//Use OpenInventor dynamic library
IV_DYNAMIC:BOOL=ON
//OpenInventor/Coin include directory
IV_INCLUDE_DIR:PATH=/usr/local/include
//OpenInventor/Coin lib directory
IV_LINK_DIR:PATH=/usr/local/lib
//Single output directory for building all libraries.
LIBRARY_OUTPUT_PATH:PATH=
//Molekel Qt moc headers
MOC_HEADER_FILES:PATH=molekel_moc_headers.cmake
//Use OpenMOIV dynamic library
MOIV_DYNAMIC:BOOL=ON
//OpenMOIV installation directory
MOIV_INCLUDE_DIR:PATH=/apps/molekel_related/OpenMOIV.src.1.0.3/include
//OpenMOIV installation directory
MOIV_LINK_DIR:PATH=/apps/molekel_related/OpenMOIV.src.1.0.3
//Molekel source file list
MOLEKEL_SRCS:PATH=molekel_sources.cmake
//Value Computed by CMake
Molekel_BINARY_DIR:STATIC=/apps/molekel_src_5.2/build
//Value Computed by CMake
Molekel_SOURCE_DIR:STATIC=/apps/molekel_src_5.2/src
//OpenBabel include directory
OPENBABEL_INCLUDE_DIR:PATH=/apps/molekel_related/openbabel-2.1.1/include
//OpenBabel lib directory
OPENBABEL_LINK_DIR:PATH=/apps/molekel_related/openbabel-2.1.1/src
//Path to a file.
OPENGL_INCLUDE_DIR:PATH=/usr/include
//Path to a library.
OPENGL_gl_LIBRARY:FILEPATH=/usr/lib64/libGL.so
//Path to a library.
OPENGL_glu_LIBRARY:FILEPATH=/usr/lib64/libGLU.so
//Path to a file.
OPENGL_xmesa_INCLUDE_DIR:PATH=/usr/include
//The location of the Qt docs
QT_DOC_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/doc
//Path to a library.
QT_FONTCONFIG_LIBRARY:FILEPATH=/usr/lib64/libfontconfig.so
//Path to a library.
QT_FREETYPE_LIBRARY:FILEPATH=/usr/lib64/libfreetype.so
//Missing description
QT_INCLUDE_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/include
//Qt library dir
QT_LIBRARY_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/lib
//The location of the Qt mkspecs
QT_MKSPECS_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/mkspecs
//The moc executable
QT_MOC_EXECUTABLE:FILEPATH=/usr/local/Trolltech/Qt-4.3.0/bin/moc
//The location of the Qt plugins
QT_PLUGINS_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/plugins
//Path to a library.
QT_PNG_LIBRARY:FILEPATH=/usr/lib64/libpng.so
//Path to a program.
QT_QMAKE_EXECUTABLE:FILEPATH=/apps/molekel_related/qt-x11-opensource-src-4.3.0/bin/qmake
//Path to a file.
QT_QT3SUPPORT_INCLUDE_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/include/Qt3Support
//The Qt QT3SUPPORT library
QT_QT3SUPPORT_LIBRARY:FILEPATH=/usr/local/Trolltech/Qt-4.3.0/lib/libQt3Support.so
//Path to a library.
QT_QT3SUPPORT_LIBRARY_DEBUG:FILEPATH=QT_QT3SUPPORT_LIBRARY_DEBUG-NOTFOUND
//Path to a library.
QT_QT3SUPPORT_LIBRARY_RELEASE:FILEPATH=/usr/local/Trolltech/Qt-4.3.0/lib/libQt3Support.so
//Path to a file.
QT_QTASSISTANT_INCLUDE_DIR:PATH=/usr/local/Trolltech/Qt-4.3.0/include/QtAssistant
//The Qt QTASSISTANT library
QT_QTASSISTANT_LIBRARY:FILEPATH=/usr/local/Trolltech/Qt-4.3.0/lib/libQtAssistantClient.so
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//Path to a file.
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QT_QTNSPLUGIN_LIBRARY_RELEASE:FILEPATH=QT_QTNSPLUGIN_LIBRARY_RELEASE-NOTFOUND
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QT_QTSVG_LIBRARY_DEBUG:FILEPATH=QT_QTSVG_LIBRARY_DEBUG-NOTFOUND
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Hi,
the problem is that OpenMOIV was built with fl fonts support. Building OpenMOIV with -Dno_libFL:int=1 should fix the problem.
E.g.
cmake -Dshared:int=1 -Dno_libFL:int=1 -Dcoin:int=1 -Dsys_fonts:int=1
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