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

[Georgi Gerganov]

Hi Sonal,

Try the following:
Open the "GNUmakefile" in your gate home directory and edit the following
block:

=================================================
ifdef G4ANALYSIS_USE_ROOT
CPPFLAGS += -DG4ANALYSIS_USE_ROOT -D_REENTRANT -I$(ROOTSYS)/include
ifdef G4ANALYSIS_USE_ROOT_PLOTTER
CPPFLAGS += -DG4ANALYSIS_USE_ROOT_PLOTTER
endif
EXTRALIBS += -L$(ROOTSYS)/lib \
-lCore -lCint \
-lHist -lGraf -lGraf3d -lGpad \
-lTree -lRint -lPostscript \
-lMatrix -lPhysics \
-lm -ldl -lpthread -rdynamic
endif
==================================================

it should look like this:
==================================================
ifdef G4ANALYSIS_USE_ROOT
CPPFLAGS += -DG4ANALYSIS_USE_ROOT -D_REENTRANT -I$(ROOTSYS)/include
ifdef G4ANALYSIS_USE_ROOT_PLOTTER
CPPFLAGS += -DG4ANALYSIS_USE_ROOT_PLOTTER
endif
EXTRALIBS += -L$(ROOTSYS)/lib \
-lCore -lCint \
-lHist -lGraf -lGraf3d -lGpad \
-lTree -lRint -lPostscript \
-lMatrix -lPhysics \
-lm -ldl -lpthread -rdynamic \
-lRIO -lRMySQL -lNet
endif
=================================================

This worked for me.
Good luck!
Georgi

On 4/14/08, Sonal Ambwani <ambwani at bu.edu> wrote:
>
> 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
>
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