[Gate-users] Question in installing Gate_v6.1

Didier BENOIT benoit at imnc.in2p3.fr
Mon Oct 17 11:05:41 CEST 2011 

Hi,

Could you try a 'make clean' before 'make'? Tell me if you have g 
another errors during the compilation.

Kind regards,
Didier

On 10/17/2011 10:58 AM, 林威佐 wrote:
> hi Didier,
> *I just tried doing that*, and it really can solve this problem.
> But I am getting the following error.
>
> [root at IL407-WillieLin gate_v6.1]# make
> Entering source/arf ...
> GNUmakefile:8: *** missing separator.  Stop.
> source/arf finished
> Entering source/geometry ...
> GNUmakefile:8: *** missing separator.  Stop.
> source/geometry finished
> Entering source/general ...
> GNUmakefile:8: *** missing separator.  Stop.
> source/general finished
> Entering source/digits_hits ...
> GNUmakefile:8: *** missing separator.  Stop.
> source/digits_hits finished
> Entering source/physics ...
> GNUmakefile:8: *** missing separator.  Stop.
> source/physics finished
> Using granular libraries ...
> Linking Gate
> ./tmp/Linux-g++/Gate/exe/Gate.o: In function `Welcome()':
> Gate.cc:(.text+0x164): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x182): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x212): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x232): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x2d1): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x2f4): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x39f): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x3c5): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x470): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x496): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x541): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x567): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x612): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x638): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x6e3): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x709): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x7b4): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x7da): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text+0x87f): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0x957): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0xa2f): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0xb0d): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text+0xbed): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> ./tmp/Linux-g++/Gate/exe/Gate.o:Gate.cc:(.text+0xccd): more undefined 
> references to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)' follow
> ./tmp/Linux-g++/Gate/exe/Gate.o: In function 
> `G4VisExecutive::RegisterGraphicsSystems()':
> Gate.cc:(.text._ZN14G4VisExecutive23RegisterGraphicsSystemsEv[G4VisExecutive::RegisterGraphicsSystems()]+0x32a): 
> undefined reference to `G4RayTracerX::G4RayTracerX()'
> ./tmp/Linux-g++/Gate/exe/Gate.o: In function `main':
> Gate.cc:(.text.startup+0x19): undefined reference to 
> `GateMessageManager::GetInstance()'
> Gate.cc:(.text.startup+0x82): undefined reference to 
> `GateSteppingVerbose::GateSteppingVerbose()'
> Gate.cc:(.text.startup+0x91): undefined reference to 
> `GateRandomEngine::instance'
> Gate.cc:(.text.startup+0xb3): undefined reference to 
> `GateSignalHandler::Install()'
> Gate.cc:(.text.startup+0xc8): undefined reference to 
> `GateRunManager::GateRunManager()'
> Gate.cc:(.text.startup+0xdf): undefined reference to 
> `GateROOTBasicOutput::GateROOTBasicOutput()'
> Gate.cc:(.text.startup+0xf4): undefined reference to 
> `GateDetectorConstruction::GateDetectorConstruction()'
> Gate.cc:(.text.startup+0xfb): undefined reference to 
> `GatePhysicsList::singleton'
> Gate.cc:(.text.startup+0x139): undefined reference to 
> `GateUserActions::GateUserActions(GateRunManager*, GateRecorderBase*)'
> Gate.cc:(.text.startup+0x143): undefined reference to 
> `GateMessageManager::EnableG4Messages(bool)'
> Gate.cc:(.text.startup+0x19c): undefined reference to 
> `GateMessageManager::EnableG4Messages(bool)'
> Gate.cc:(.text.startup+0x1a4): undefined reference to 
> `GateRunManager::InitializeAll()'
> Gate.cc:(.text.startup+0x1b9): undefined reference to 
> `GatePrimaryGeneratorAction::GatePrimaryGeneratorAction()'
> Gate.cc:(.text.startup+0x1cb): undefined reference to 
> `GateOutputMgr::m_digiMode'
> Gate.cc:(.text.startup+0x1d2): undefined reference to 
> `GateOutputMgr::instance'
> Gate.cc:(.text.startup+0x1ed): undefined reference to 
> `GateDigitizer::GetInstance()'
> Gate.cc:(.text.startup+0x21e): undefined reference to 
> `GatePulseProcessorChain::GatePulseProcessorChain(GateDigitizer*, 
> G4String const&)'
> Gate.cc:(.text.startup+0x233): undefined reference to 
> `GateDigitizer::StoreNewPulseProcessorChain(GatePulseProcessorChain*)'
> Gate.cc:(.text.startup+0x243): undefined reference to 
> `GateSourceMgr::mInstance'
> Gate.cc:(.text.startup+0x256): undefined reference to 
> `GateApplicationMgr::instance'
> Gate.cc:(.text.startup+0x269): undefined reference to 
> `GateClock::pInstance'
> Gate.cc:(.text.startup+0x281): undefined reference to 
> `GateClock::SetTime(double)'
> Gate.cc:(.text.startup+0x296): undefined reference to 
> `GateUIcontrolMessenger::GateUIcontrolMessenger()'
> Gate.cc:(.text.startup+0x34f): undefined reference to 
> `GateSourceMgr::~GateSourceMgr()'
> Gate.cc:(.text.startup+0x382): undefined reference to 
> `GateRandomEngine::~GateRandomEngine()'
> Gate.cc:(.text.startup+0x429): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text.startup+0x469): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text.startup+0x5a8): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text.startup+0x5d0): undefined reference to 
> `GateMessageManager::GetSpace(int)'
> Gate.cc:(.text.startup+0x692): undefined reference to 
> `GateClock::GateClock()'
> Gate.cc:(.text.startup+0x6af): undefined reference to 
> `GatePhysicsList::GatePhysicsList()'
> Gate.cc:(.text.startup+0x6e9): undefined reference to 
> `GateOutputMgr::GateOutputMgr(G4String)'
> Gate.cc:(.text.startup+0x71f): undefined reference to 
> `GateRandomEngine::GateRandomEngine()'
> Gate.cc:(.text.startup+0x731): undefined reference to 
> `GateHitFileReader::GetInstance()'
> Gate.cc:(.text.startup+0x74b): undefined reference to 
> `GateSourceMgr::GateSourceMgr()'
> Gate.cc:(.text.startup+0x768): undefined reference to 
> `GateApplicationMgr::GateApplicationMgr()'
> Gate.cc:(.text.startup+0x799): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> Gate.cc:(.text.startup+0x87b): undefined reference to 
> `GateMessageManager::GetMessageLevel(std::basic_string<char, 
> std::char_traits<char>, std::allocator<char> >)'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenGL.a(G4OpenGLXmViewer.o): 
> In function `G4OpenGLXmViewer::~G4OpenGLXmViewer()':
> G4OpenGLXmViewer.cc:(.text+0x65): undefined reference to 
> `G4Xt::getInstance()'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenGL.a(G4OpenGLXmViewer.o): 
> In function `G4OpenGLXmViewer::ShowView()':
> G4OpenGLXmViewer.cc:(.text+0x155): undefined reference to 
> `G4Xt::getInstance()'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenGL.a(G4OpenGLXmViewer.o): 
> In function `G4OpenGLXmViewer::~G4OpenGLXmViewer()':
> G4OpenGLXmViewer.cc:(.text+0x1d66): undefined reference to 
> `G4Xt::getInstance()'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenGL.a(G4OpenGLXmViewer.o): 
> In function `G4OpenGLXmViewer::GetXmConnection()':
> G4OpenGLXmViewer.cc:(.text+0x1de5): undefined reference to 
> `G4Xt::getInstance()'
> G4OpenGLXmViewer.cc:(.text+0x2005): undefined reference to 
> `G4Xt::PutStringInResourceDatabase(char*)'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenGL.a(G4OpenGLXmMainMenubarCallbacks.o): 
> In function `G4OpenGLXmViewer::misc_callback(_WidgetRec*, void*, void*)':
> G4OpenGLXmMainMenubarCallbacks.cc:(.text+0x201): undefined reference 
> to `G4Xt::getInstance()'
> /usr/bin/src/GATE/geant4.9.4.p02/lib/Linux-g++/libG4OpenInventor.a(G4OpenInventorXt.o): 
> In function `G4OpenInventorXt::Initialize()':
> G4OpenInventorXt.cc:(.text+0xd1): undefined reference to 
> `G4Xt::getInstance()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVolumeID::MoveToBottomVolumeFrame(CLHEP::Hep3Vector, int) const'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateProjectionSet::FillARF(int, double, double, double)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVolumeManager::singleton_VolumeManager'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVolumeManager::GateVolumeManager()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVolumeID::GateVolumeID(G4TouchableHistory const*)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateOutputMgr::GetModule(G4String)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVolumeID::GetCreatorDepth(G4String) const'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVOutputModule::~GateVOutputModule()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVOutputModule::Describe(unsigned long)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateOutputModuleMessenger::~GateOutputModuleMessenger()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to `typeinfo for 
> GateMessenger'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateSystemListManager::FindSystemOfCreator(GateVVolume*)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateVOutputModule::GateVOutputModule(G4String const&, GateOutputMgr*, 
> DigiMode)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateMessenger::GateMessenger(G4String const&, bool)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to `typeinfo for 
> GateOutputModuleMessenger'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateMessenger::~GateMessenger()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateBox::GateBox(G4String const&, bool, int)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to `typeinfo for 
> GateVOutputModule'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateOutputModuleMessenger::GateOutputModuleMessenger(GateVOutputModule*)'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateSystemListManager::GetInstance()'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to `typeinfo for 
> GateToProjectionSet'
> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to 
> `GateOutputModuleMessenger::SetNewValue(G4UIcommand*, G4String)'
> collect2: ld return 1
> make: *** [bin/Linux-g++/Gate] Error 1
>
> Any help would be appreciated.
> Thank you for your time,
> willie
>
>
>
>
>
>
> 2011/10/17 Didier BENOIT <benoit at imnc.in2p3.fr 
> <mailto:benoit at imnc.in2p3.fr>>
>
>     Hi,
>
>     It seems you don't link with the ROOT libraries. You have to
>     indicate where is the ROOT libraries in the 'env_gate.sh' for
>     instance, with the following command:
>     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${ROOTSYS}/lib
>
>     Kind regards,
>     Didier
>
>
>     On 10/17/2011 10:09 AM, 林威佐 wrote:
>
>         Dear Gaters,
>         I am trying to install the newest version of GATE_v6.1 but I
>         am having a
>         really annoying problem.
>         My
>         system<http://answerpot.com/showthread.php?2291247-Gate_v6.1+installation+problem#>is
>
>
>         Fedora15, geant4.9.4.p02. CLHEP.2.1.0.1
>         All seems to be fine installed until I am going to install
>         GATE and do
>         "make",
>         I am getting the following error. Could anyone help me about this?
>
>         [willielin at IL407-WillieLin gate_v6.1]# make
>         Entering source/arf ...
>         GNUmakefile:8: *** missing separator.  Stop.
>         source/arf finished
>         Entering source/geometry ...
>         GNUmakefile:8: *** missing separator.  Stop.
>         source/geometry finished
>         Entering source/general ...
>         GNUmakefile:8: *** missing separator.  Stop.
>         source/general finished
>         Entering source/digits_hits ...
>         GNUmakefile:8: *** missing separator.  Stop.
>         source/digits_hits finished
>         Entering source/physics ...
>         GNUmakefile:8: *** missing separator.  Stop.
>         source/physics finished
>         Using granular libraries ...
>         Linking Gate
>         /usr/bin/ld: cannot find -lCore
>         /usr/bin/ld: cannot find -lCint
>         /usr/bin/ld: cannot find -lRIO
>         /usr/bin/ld: cannot find -lNet
>         /usr/bin/ld: cannot find -lHist
>         /usr/bin/ld: cannot find -lGraf
>         /usr/bin/ld: cannot find -lGraf3d
>         /usr/bin/ld: cannot find -lGpad
>         /usr/bin/ld: cannot find -lTree
>         /usr/bin/ld: cannot find -lRint
>         /usr/bin/ld: cannot find -lPostscript
>         /usr/bin/ld: cannot find -lMatrix
>         /usr/bin/ld: cannot find -lPhysics
>         /usr/bin/ld: cannot find -lMathCore
>         /usr/bin/ld: cannot find -lThread
>         collect2: ld return 1
>         make: *** [bin/Linux-g++/Gate] Error 1
>
>
>         *Any help would be appreciated.
>         Thank you for your time,*
>         willie
>         _______________________________________________
>         Gate-users mailing list
>         Gate-users at lists.opengatecollaboration.org
>         <mailto:Gate-users at lists.opengatecollaboration.org>
>         http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
>     -- 
>     ----------------------------------------------------------------
>     Didier BENOIT, GATE Engineer
>     Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
>     IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
>     Campus d’Orsay
>     Bâtiment 440
>     91406 ORSAY Cedex
>
>     Tél : (33) 1 69 15 68 76
>     E-mail : benoit at imnc.in2p3.fr <mailto:benoit at imnc.in2p3.fr>
>     http://www.imnc.in2p3.fr
>     ----------------------------------------------------------------
>
>


-- 
----------------------------------------------------------------
Didier BENOIT, GATE Engineer
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
Campus d’Orsay
Bâtiment 440
91406 ORSAY Cedex

Tél : (33) 1 69 15 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
----------------------------------------------------------------

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