[Gate-users] linking Gate after compilation fails

[Albert Hirtl]

Dear Edo,

Thanks a lot, this solved the problem! Finally I am ready to use Gate...

Thankful from Vienna,
Albert

Edoardo Pasca wrote:
> On Tue, 2009-02-24 at 08:41 +0100, Albert Hirtl wrote:
>   
>> Dear Gate users,
>>
>> I am trying to install gate_v4.0.0 on Scientific Linux 5.2 with 
>> geant4.9.1.p02, root_v5.14 and CLHEP_v2.0.3.2. However, after compiling 
>> gate, which goes fine, except for two warnings along the way:
>> --
>> Compiling GateEcatAccelSystem.cc ...
>> /opt/PETMC/ECAT/include/machine_indep.h:23: error: declaration of C 
>> function ‘void swab(const void*, void*, size_t)’ conflicts with
>> /usr/include/unistd.h:1086: error: previous declaration ‘void swab(const 
>> void*, void*, ssize_t)’ here
>>     
>
>
> It is a problem with the ECAT library. I seem to remember that you have
> to remove the definition of swab() function in the machine_indep.h . 
> In any case I send you the machine_indep.h that I used.
>
> Please, for further info read the Gate UserGuide v4.0.0 at section
> 10.6.1
>
> Edo 
>
>   
>> /opt/PETMC/clhep-2.0.3.2/include/CLHEP/Units/PhysicalConstants.h:78: 
>> warning: ‘CLHEP::electron_charge’ defined but not used
>> /opt/PETMC/clhep-2.0.3.2/include/CLHEP/Random/Randomize.h:67: warning: 
>> ‘CLHEP::HepRandomGenActive’ defined but not used
>> make[1]: *** [../../tmp/Linux-g++/Gate/GateEcatAccelSystem.o] Error 1
>> --
>>
>> and
>>
>> --
>> Compiling GateSinoAccelToEcat7.cc ...
>> /opt/PETMC/ECAT/include/machine_indep.h:23: error: declaration of C 
>> function ‘void swab(const void*, void*, size_t)’ conflicts with
>> /usr/include/unistd.h:1086: error: previous declaration ‘void swab(const 
>> void*, void*, ssize_t)’ here
>> /opt/PETMC/clhep-2.0.3.2/include/CLHEP/Units/PhysicalConstants.h:78: 
>> warning: ‘CLHEP::electron_charge’ defined but not used
>> /opt/PETMC/clhep-2.0.3.2/include/CLHEP/Random/Randomize.h:67: warning: 
>> ‘CLHEP::HepRandomGenActive’ defined but not used
>> make[1]: *** [../../tmp/Linux-g++/Gate/GateSinoAccelToEcat7.o] Error 1
>> --
>>
>> the following problem occurs during linking Gate:
>>
>> ----
>> source/management finished
>> Using granular libraries ...
>> Linking Gate ...
>> ./tmp/Linux-g++/Gate/libGate.a(GateDetectorConstruction.o): In function 
>> `GateDetectorConstruction::BuildSurfaces()':
>> GateDetectorConstruction.cc:(.text+0x189): undefined reference to 
>> `GateObjectCreatorStore::GetInstance()'
>> GateDetectorConstruction.cc:(.text+0x1a6): undefined reference to 
>> `GateSurfaceList::BuildSurfaces()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateDetectorConstruction.o): In function 
>> `GateDetectorConstruction::GateDetectorConstruction()':
>> GateDetectorConstruction.cc:(.text+0x637): undefined reference to 
>> `GateObjectCreatorStore::GetInstance()'
>> GateDetectorConstruction.cc:(.text+0x63f): undefined reference to 
>> `GateSystemListManager::GetInstance()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateDetectorConstruction.o): In function 
>> `GateDetectorConstruction::GateDetectorConstruction()':
>> GateDetectorConstruction.cc:(.text+0xb97): undefined reference to 
>> `GateObjectCreatorStore::GetInstance()'
>> GateDetectorConstruction.cc:(.text+0xb9f): undefined reference to 
>> `GateSystemListManager::GetInstance()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateDigitizer.o): In function 
>> `GateDigitizer::~GateDigitizer()':
>> GateDigitizer.cc:(.text+0x2042): undefined reference to `vtable for 
>> GateNamedObject'
>> GateDigitizer.cc:(.text+0x214b): undefined reference to `vtable for 
>> GateNamedObject'
>>
>>
>> ..... lots of error messages of the same kind ....
>>
>> GateArrayRepeaterMessenger.cc:(.text+0x39d): undefined reference to 
>> `GateObjectRepeaterMessenger::SetNewValue(G4UIcommand*, G4String)'
>> ./tmp/Linux-g++/Gate/libGate.a(GateArrayRepeaterMessenger.o): In 
>> function 
>> `GateArrayRepeaterMessenger::GateArrayRepeaterMessenger(GateArrayRepeater*)':
>> GateArrayRepeaterMessenger.cc:(.text+0x51a): undefined reference to 
>> `GateObjectRepeaterMessenger::GateObjectRepeaterMessenger(GateVObjectRepeater*)'
>> GateArrayRepeaterMessenger.cc:(.text+0xa31): undefined reference to 
>> `GateObjectRepeaterMessenger::~GateObjectRepeaterMessenger()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateArrayRepeaterMessenger.o): In 
>> function 
>> `GateArrayRepeaterMessenger::GateArrayRepeaterMessenger(GateArrayRepeater*)':
>> GateArrayRepeaterMessenger.cc:(.text+0xdaa): undefined reference to 
>> `GateObjectRepeaterMessenger::GateObjectRepeaterMessenger(GateVObjectRepeater*)'
>> GateArrayRepeaterMessenger.cc:(.text+0x12c1): undefined reference to 
>> `GateObjectRepeaterMessenger::~GateObjectRepeaterMessenger()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateArrayRepeaterMessenger.o): In 
>> function `GateArrayRepeaterMessenger::~GateArrayRepeaterMessenger()':
>> GateArrayRepeaterMessenger.cc:(.text+0x116): undefined reference to 
>> `GateObjectRepeaterMessenger::~GateObjectRepeaterMessenger()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateArrayRepeaterMessenger.o): In 
>> function `GateArrayRepeaterMessenger::~GateArrayRepeaterMessenger()':
>> GateArrayRepeaterMessenger.cc:(.text+0x196): undefined reference to 
>> `GateObjectRepeaterMessenger::~GateObjectRepeaterMessenger()'
>> ./tmp/Linux-g++/Gate/libGate.a(GateArrayRepeaterMessenger.o):(.rodata._ZTI26GateArrayRepeaterMessenger[typeinfo 
>> for GateArrayRepeaterMessenger]+0x8): undefined reference to `typeinfo 
>> for GateObjectRepeaterMessenger'
>> collect2: ld returned 1 exit status
>> make: *** [bin/Linux-g++/Gate] Error 1
>>
>> ----
>>
>> Does anybody have an idea what is going wrong? I am somewhat desperate, 
>> since I already tried lots of things and I am running out of ideas.
>> Help would be very much appreciated!
>>
>> Cheers,
>> Albert
>>
>>     


-- 
Albert Hirtl

Medizinische Universität Wien
Universitätsklinik für Nuklearmedizin
Allgemeines Krankenhaus Wien
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 5545

Web: http://www.meduniwien.ac.at/nuklear/

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