[Gate-users] Question in installing Gate_v6.1

Ernest Galbrun ernest.galbrun at ensem.inpl-nancy.fr
Mon Oct 17 18:36:24 CEST 2011 

I had the same issue when installing gate and I had to add the following
line to the .gmk file :
LDFLAGS += -L/path/to/root/lib

(the LD_LIBRARY_PATH is for dynamic linking when running the application,
not for linking with ld)

regards,
-- 
*Ernest Galbrun*
Ingénieur de recherche ENSEM / CRAN
2, avenue de la forêt de Haye - 54516 Vandœuvre lès Nancy
Tél : +33/0 3 83 59 55 41 - Mobile : +33/0 6 28 08 60 14 - Fax : +33/0 3 83
59 56 44




On Mon, Oct 17, 2011 at 11:05, Didier BENOIT <benoit at imnc.in2p3.fr> wrote:

> 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._**ZN14G4VisExecutive23RegisterGr**aphicsSystemsEv[**
>> 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#<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<Gate-users at lists.opengatecollaboration.org>
>>        <mailto:Gate-users at lists.**opengatecollaboration.org<Gate-users at lists.opengatecollaboration.org>
>> >
>>
>>        http://lists.**opengatecollaboration.org/**
>> mailman/listinfo/gate-users<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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>

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