[Gate-users] Linking error during Gate Installation : Please help

[Sonal Ambwani]

Dear Gate users :

I have been trying to compile GATE on a 64bit redhat linux environment, 
and the following are the errors that I get when the make process 
terminates :

Linking Gate ...
/home/sonal/gate/tmp/Linux-g++/Gate/libGate.a(GateHitFileReader.o)(.text+0x39c): In function 
`GateHitFileReader::PrepareAcquisition()':
GateHitFileReader.cc: undefined reference to `TFile::TFile(char const*, 
char const*, char const*, int)'
/home/sonal/gate/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o)(.text+0x223c): In 
function `GateToRoot::RecordBeginOfAcquisition()':
GateToRoot.cc: undefined reference to `TFile::TFile(char const*, char 
const*, char const*, int)'
/home/sonal/gate/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o)(.text+0x244e):GateToRoot.cc: undefined reference to `TFile::TFile(char const*, char const*, char const*, 
int)'
/home/sonal/gate/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o)(.text+0x2ef5): In 
function `GateToRoot::RecordVoxels(GateVGeometryVoxelStore*)':
GateToRoot.cc: undefined reference to `TFile::TFile(char const*, char 
const*, char const*, int)'
/home/sonal/root/lib/libHist.so: undefined reference to `TMath::Nint(double)'
/home/sonal/root/lib/libTree.so: undefined reference to `vtable for TSQLRow'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TFileCacheRead::TFileCacheRead(TFile*, int)'
/home/sonal/root/lib/libHist.so: undefined reference to 
`ROOT::Math::GaussIntegratorOneDim::Integral(double, double)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadArray(double*&)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadArray(int*&)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadStaticArray(char*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::WriteArray(bool const*, int)'
/home/sonal/root/lib/libHist.so: undefined reference to 
`TMath::ErfInverse(double)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadArrayFloat16(float*&, TStreamerElement*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadArray(float*&)'
.
.
.
.

/home/sonal/root/lib/libGraf3d.so: undefined reference to 
`TMath::Normalize(float*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadFloat16(float*, TStreamerElement*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadStaticArray(int*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::ReadStaticArray(short*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TFile::GetCacheRead() const'
/home/sonal/root/lib/libHist.so: undefined reference to 
`ROOT::Math::GaussLegendreIntegrator::~GaussLegendreIntegrator()'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TSQLRow::Streamer(TBuffer&)'
/home/sonal/root/lib/libHist.so: undefined reference to 
`ROOT::Math::RichardsonDerivator::~RichardsonDerivator()'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::CheckObject(void const*, TClass const*)'
/home/sonal/root/lib/libTree.so: undefined reference to `int 
TStreamerInfo::ReadBuffer<char**>(TBuffer&, char** const&, int, int, 
int, int)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TBufferFile::DecrementLevel(TVirtualStreamerInfo*)'
/home/sonal/root/lib/libTree.so: undefined reference to 
`TFileCacheRead::TFileCacheRead()'
/home/sonal/root/lib/libHist.so: undefined reference to 
`TMath::Gaus(double, double, double, bool)'
/home/sonal/root/lib/libHist.so: undefined reference to 
`TMath::Gamma(double, double)'
/home/sonal/root/lib/libHist.so: undefined reference to `TRandom3::Rndm(int)'
/home/sonal/root/lib/libGraf.so: undefined reference to 
`ROOT::Fit::BinData::Add(double, double, double, double, double)'
/home/sonal/root/lib/libTree.so: undefined reference to `typeinfo for 
TEmulatedCollectionProxy'
collect2: ld returned 1 exit status
make: *** [/home/sonal/gate/bin/Linux-g++/Gate] Error 1


Can someone pinpoint the cause of this failure?
Thanks.
Sonal



Quoting Wolfram Stiller <w.stiller at dkfz-heidelberg.de>:

> Dear Sonal,
>
> On Friday 11 April 2008 23:10, Sonal Ambwani wrote:
>
>> I am getting the following errors during the make process of Gate
>> installation :
>>
>> Linking Gate ...
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.so when
>> searching for -lXt
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when
>> searching for -lXt
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libGLU.so when
>> searching for -lGLU
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libGLU.a when
>> searching for -lGLU
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXmu.so when
>> searching for -lXmu
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXmu.a when
>> searching for -lXmu
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.so when
>> searching for -lXt
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when
>> searching for -lXt
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXext.so when
>> searching for -lXext
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXext.a when
>> searching for -lXext
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when
>> searching for -lX11
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when
>> searching for -lX11
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libSM.so when
>> searching for -lSM
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libSM.a when
>> searching for -lSM
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libICE.so when
>> searching for -lICE
>> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libICE.a when
>> searching for -lICE
>>
>>
>> Please help me fix this issue. It's apparent that there is a clash
>> between the 32 bit and the 64 bit libraries...
>
> these messages are no errors and just tell you that the 32bit 
> libraries (which
> by default are installed in addition to the 64bit libraries when installing a
> 64bit linux system) where skipped when linking the program - you probably
> have a 64bit linux system installed. If the 32bit libraries are in your
> library path the linker will find these, notice they are 32 bit (and
> thus "incompatible") and link against the 64bit libraries (if they are in
> your library path).
>
>> but I am not sure how to go about correcting it.
>
> Thus there is no need to correct anything, just as long as the 
> linking process
> does not return any errors. In case you get an error message from the linker,
> you should post that one instead, the lines above are just an information
> from the linker.
>
>> Thanks in advance,
>
> Hope it helps.
>
> Regards
>
> Wolf
>
>
>
> :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
>
> Dipl. Phys. Wolfram Stiller
>
> German Cancer Research Center (DKFZ)
> Dept. of Medical Physics in Radiology (E020)
> Im Neuenheimer Feld 280
> D-69120 Heidelberg
> Germany
>
> Tel.: +49 (0) 6221 42 2468
> Fax:  +49 (0) 6221 42 2572
>
> E-mail: w.stiller at dkfz.de
>         wolfram.stiller at dkfz.de
>
>
>
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Sonal Ambwani

Dept. of Electrical and Computer Engineering
Boston University