[Gate-users] Trouble installing GATE
Tuan
huynht4 at mcmaster.ca
Mon Feb 14 21:58:22 CET 2011
Hi Didier,
That solved the problem with TROOT.h. Thanks a lot. But I still get
the following message:
tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ 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
Creating shared library tmp/Linux-g++/Gate/libGate.so ...
g++: *.o: No such file or directory
make: *** [tmp/Linux-g++/Gate/libGate.so] Error 1
tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$
I don't know what to do about that.
Cheers,
Tuan Huynh
On Mon, 2011-02-14 at 21:45 +0100, Didier Benoit wrote:
> Hi Tuan,
>
>
> In the GateCommon.gmk file, could you add this line: CPPFLAGS += -I
> $(ROOTSYS)/include, for me the problem is "TROOT.h: No such file or
> directory" a path is wrong somewhere.
>
>
> Kind Regards,
> Didier
>
>
>
> On Feb 14, 2011, at 3:55 PM, Tuan wrote:
>
> > Hi Didier,
> >
> > I just tried doing that, but it still gives the exact same error.
> >
> > Thanks,
> > Tuan Huynh
> >
> > On Sat, 2011-02-12 at 12:00 +0100,
> > gate-users-request at lists.opengatecollaboration.org wrote:
> > > Send Gate-users mailing list submissions to
> > > gate-users at lists.opengatecollaboration.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > > or, via email, send a message with subject or body 'help' to
> > > gate-users-request at lists.opengatecollaboration.org
> > >
> > > You can reach the person managing the list at
> > > gate-users-owner at lists.opengatecollaboration.org
> > >
> > > When replying, please edit your Subject line so it is more
> > > specific
> > > than "Re: Contents of Gate-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: Trouble installing GATE (Didier Benoit)
> > > 2. Re: ASCII coincidence.dat (Nicolas GUIGNARD)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Fri, 11 Feb 2011 15:49:24 +0100
> > > From: Didier Benoit <benoit at imnc.in2p3.fr>
> > > To: Tuan <huynht4 at mcmaster.ca>
> > > Cc: gate-users at lists.opengatecollaboration.org
> > > Subject: Re: [Gate-users] Trouble installing GATE
> > > Message-ID: <4D554C74.1010408 at imnc.in2p3.fr>
> > > Content-Type: text/plain; charset=windows-1252; format=flowed
> > >
> > > Hi Tuan,
> > >
> > > Your GATEHOME should be: /home/tuan/GATE_ROOT/gate_v6.0_p01, I
> > > think
> > > In your PATH variable it's better:
> > > export PATH=$PATH:$ROOTSYS/bin:$GATEHOME/bin
> > >
> > > Kind Regards,
> > > Didier
> > >
> > > On 02/11/2011 03:41 PM, Tuan wrote:
> > > > Hi,
> > > >
> > > > I thought I already set all the environment variables in the
> > > > env_gate.sh
> > > > file like so:
> > > >
> > > > export GATEHOME=/home/tuan/GATE_ROOT
> > > > export G4INSTALL=/home/tuan/GATE_ROOT/geant4.9.2.p04
> > > > export G4VERSION=9.2
> > > > export ROOTSYS=/home/tuan/GATE_ROOT/root
> > > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:
> > > > $ROOTSYS/lib:/home/tuan/GATE_ROOT/2.0.4.2/lib
> > > > export PATH=$PATH:$ROOTSYS/lib:$GATEHOME/bin/$G4SYSTEM
> > > >
> > > > Is that incorrect? Is there something else I'm missing?
> > > >
> > > > Thanks,
> > > > Tuan Huynh
> > > >
> > > >
> > > > > Message: 5
> > > > > Date: Thu, 10 Feb 2011 21:14:19 +0100
> > > > > From: Alexandre Dupas<alexandre.dupas at gmail.com>
> > > > > To: gate-users at lists.opengatecollaboration.org
> > > > > Subject: Re: [Gate-users] Trouble installing GATE
> > > > > Message-ID:
> > > > > <AANLkTikWpT8beyrv0NxHwCPGcDFcya7zXTEfRN_Mb3jQ at mail.gmail.com>
> > > > > Content-Type: text/plain; charset=UTF-8
> > > > >
> > > > > Hello,
> > > > >
> > > > > Actually, you have to define some environment variables to
> > > > > allow the
> > > > > build system to retrieve the root install directory.
> > > > >
> > > > > The main variable is ROOTSYS that you can define using
> > > > >
> > > > > export ROOTSYS=/path/to/root/installation/directory
> > > > >
> > > > > See for more details the "Setting environment variable"
> > > > > section of the
> > > > > following page :
> > > > > http://minos.phy.bnl.gov/software/rug/rug26.html
> > > > >
> > > > > I hope this help,
> > > > >
> > > > > Best regards,
> > > > > Alexandre
> > > > > --
> > > > > Alexandre Dupas
> > > > > Postdoctoral Research Fellow
> > > > > INSERM U698, Bich?t M?decine Nucl?aire
> > > > >
> > > > > 2011/2/10 Tuan<huynht4 at mcmaster.ca>:
> > > > > > Hi,
> > > > > >
> > > > > > ? ? I. I've been trying to install GATE on a new
> > > > > > system. ?I've followed
> > > > > > ? ? ? ?the instructions on the Installation Guide to the
> > > > > > letter but I
> > > > > > ? ? ? ?keep getting this error when I use make:
> > > > > >
> > > > > > tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ source
> > > > > > env_gate.sh
> > > > > >
> > > > > > The current value of G4INSTALL
> > > > > > is: /home/tuan/GATE_ROOT/geant4.9.2.p04
> > > > > > The current value of G4VERSION is: 9.2
> > > > > >
> > > > > > Launching Geant4 configuration
> > > > > > script /home/tuan/GATE_ROOT/geant4.9.2.p04/env.sh
> > > > > >
> > > > > > On this machine the G4SYSTEM=Linux-g++
> > > > > > On this machine the
> > > > > > G4INSTALL=/home/tuan/GATE_ROOT/geant4.9.2.p04
> > > > > > On this machine the
> > > > > > G4INCLUDE=/home/tuan/GATE_ROOT/geant4.9.2.p04/include/
> > > > > > On this machine the
> > > > > > G4LIB=/home/tuan/GATE_ROOT/geant4.9.2.p04/lib
> > > > > > On this machine the
> > > > > > G4LEVELGAMMADATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/PhotonEvaporation2.0
> > > > > > On this machine the
> > > > > > G4RADIOACTIVEDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/RadioactiveDecay3.2
> > > > > > On this machine the
> > > > > > G4LEDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4EMLOW6.2
> > > > > > On this machine the
> > > > > > G4NEUTRONHPDATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4NDL3.13
> > > > > > On this machine the
> > > > > > G4ABLADATA=/home/tuan/GATE_ROOT/geant4.9.2.p04/data/G4ABLA3.0
> > > > > > On this machine the
> > > > > > CLHEP_BASE_DIR=/home/tuan/GATE_ROOT/2.0.4.2
> > > > > > On this machine the
> > > > > > CLHEP_INCLUDE_DIR=/home/tuan/GATE_ROOT/2.0.4.2/include
> > > > > > On this machine the
> > > > > > CLHEP_LIB_DIR=/home/tuan/GATE_ROOT/2.0.4.2/lib
> > > > > > On this machine the CLHEP_LIB=CLHEP
> > > > > > On this machine the G4UI_USE_TCSH=1
> > > > > > On this machine the G4VIS_BUILD_OPENGLX_DRIVER=1
> > > > > > On this machine the G4VIS_USE_OPENGLX=1
> > > > > > On this machine the XMFLAGS=
> > > > > > On this machine the XMLIBS=
> > > > > > On this machine the XMFLAGS=
> > > > > > On this machine the XAWFLAGS=
> > > > > > On this machine the XAWLIBS=
> > > > > > On this machine the G4LIB_BUILD_STATIC=1
> > > > > > On this machine the G4LIB_USE_GRANULAR=1
> > > > > >
> > > > > > Configuring GATE options
> > > > > >
> > > > > > G4WORKDIR set to .
> > > > > > G4TMP set to ./tmp
> > > > > > G4BIN set to ./bin
> > > > > > Data analysis and output features enabled
> > > > > > Ascii data output enabled
> > > > > > Transport and generation of optical photons is disabled
> > > > > > Checking your LD_LIBRARY_PATH variable...
> > > > > > ?==> OK: /home/tuan/GATE_ROOT/root/lib is already in your
> > > > > > LD_LIBRARY_PATH
> > > > > > Use of ROOT enabled
> > > > > > ROOT real-time plotter disabled
> > > > > > LMF data output disabled
> > > > > > ECAT7 data output disabled
> > > > > > GATEHOME is set to /home/tuan/GATE_ROOT
> > > > > > Checking your path variable...
> > > > > > ?==> OK: /home/tuan/GATE_ROOT/bin/Linux-g++ added to your
> > > > > > path variable
> > > > > > Checking your LD_LIBRARY_PATH variable...
> > > > > > ?==> OK: /home/tuan/GATE_ROOT/tmp/Linux-g++/Gate added to
> > > > > > your path
> > > > > > variable
> > > > > > G4VERSION9_2 is set: GATE is compatible with the geant4
> > > > > > version 9.2
> > > > > >
> > > > > > Done
> > > > > >
> > > > > > tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$ make
> > > > > > Making dependency for file Gate.cc ...
> > > > > > ./source/physics/include/GateSourcePhaseSpace.hh:14: fatal
> > > > > > error:
> > > > > > TROOT.h: No such file or directory
> > > > > > compilation terminated.
> > > > > > 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
> > > > > > Creating shared library tmp/Linux-g++/Gate/libGate.so ...
> > > > > > g++: *.o: No such file or directory
> > > > > > make: *** [tmp/Linux-g++/Gate/libGate.so] Error 1
> > > > > > tuan at tuan-Inspiron-560:~/GATE_ROOT/gate_v6.0_p01$
> > > > > >
> > > > > > It seems like Root wasn't installed properly so I've tried
> > > > > > reinstalling
> > > > > > it a few times (different versions as well) to no
> > > > > > avail. ?What could be
> > > > > > the problem?
> > > > > >
> > > > > > Thanks,
> > > > > > Tuan Huynh
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > Gate-users mailing list
> > > > > > Gate-users at lists.opengatecollaboration.org
> > > > > > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > > > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Gate-users mailing list
> > > > Gate-users at lists.opengatecollaboration.org
> > > > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > >
> > >
> > > --
> > > ----------------------------------------------------------------
> > > Didier BENOIT, GATE Engineer
> > >
> > > Imagerie et Mod?lisation en Neurobiologie et Canc?rologie (IMNC)
> > > IMNC ? UMR 8165 CNRS ? Universit? Paris 7 ? Universit? Paris 11
> > > Campus d?Orsay
> > > B?timent 440
> > > 91405 ORSAY Cedex
> > >
> > > T?l : (33) 1 69 15 68 76
> > > E-mail : benoit at imnc.in2p3.fr
> > > http://www.imnc.in2p3.fr
> > > ----------------------------------------------------------------
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Fri, 11 Feb 2011 15:59:32 +0100
> > > From: Nicolas GUIGNARD <nicolas.guignard8 at gmail.com>
> > > To: Marcin Balcerzyk <m.balcerzyk at pluri.ucm.es>
> > > Cc: gate-users at lists.opengatecollaboration.org
> > > Subject: Re: [Gate-users] ASCII coincidence.dat
> > > Message-ID:
> > > <AANLkTin41zR6U9ag=nsphyxuRi8Y2y1VsFLaNxP4TJYE at mail.gmail.com>
> > > Content-Type: text/plain; charset=ISO-8859-1
> > >
> > > Hello Marcin
> > > many many thanks for your reply and information.
> > > Nicolas
> > >
> > > On Wed, Feb 9, 2011 at 11:28 AM, Marcin Balcerzyk
> > > <m.balcerzyk at pluri.ucm.es>wrote:
> > >
> > > > Dear Nicolas.
> > > >
> > > >
> > > >
> > > > Coincidence.dat and other ascii files have column order
> > > > described in Users
> > > > Guide. Its order depends very much on the design of your
> > > > scanner, so there
> > > > is no universal naming.
> > > >
> > > >
> > > >
> > > > In my case of scanner I have for Singles.dat the following
> > > > columns and
> > > > first row of data
> > > >
> > > > *IDRun*
> > > >
> > > > *IDEvent*
> > > >
> > > > *IDSource*
> > > >
> > > > *AnihX*
> > > >
> > > > *AnihY*
> > > >
> > > > *AnihZ*
> > > >
> > > > *VolID*
> > > >
> > > > *VolID2*
> > > >
> > > > *VolID3*
> > > >
> > > > *VolID4*
> > > >
> > > > *VolID5*
> > > >
> > > > *VolID6*
> > > >
> > > > *TimeStamp*
> > > >
> > > > *EnergyDep*
> > > >
> > > > *EventX*
> > > >
> > > > *EventY*
> > > >
> > > > *EventZ*
> > > >
> > > > *ComptPhan*
> > > >
> > > > *ComptDet*
> > > >
> > > > *ReyPhan*
> > > >
> > > > *ReyDet*
> > > >
> > > > *ComptPhanName*
> > > >
> > > > *RayPhanName*
> > > >
> > > > 0
> > > >
> > > > 5
> > > >
> > > > 0
> > > >
> > > > -6.26E+00
> > > >
> > > > -2.27E+00
> > > >
> > > > 3.57E+00
> > > >
> > > > 0
> > > >
> > > > 5
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 1.23E-06
> > > >
> > > > 5.75E-01
> > > >
> > > > -4.19E+01
> > > >
> > > > -4.05E+01
> > > >
> > > > -1.88E+01
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > NULL
> > > >
> > > > NULL
> > > >
> > > >
> > > >
> > > > For coincidence.dat it is first for 1st detector, than for 2nd
> > > > (from same
> > > > IDEVENT you can see it?s a true coincidence):
> > > >
> > > > *1IDRun*
> > > >
> > > > *1IDEvent*
> > > >
> > > > *1IDSource*
> > > >
> > > > *1AnihX*
> > > >
> > > > *1AnihY*
> > > >
> > > > *1AnihZ*
> > > >
> > > > *1TimeStamp*
> > > >
> > > > *1EnergyDep*
> > > >
> > > > *1EventX*
> > > >
> > > > *1EventY*
> > > >
> > > > *1EventZ*
> > > >
> > > > *1VolID1*
> > > >
> > > > *1VolID2*
> > > >
> > > > *1VolID3*
> > > >
> > > > *1VolID4*
> > > >
> > > > *1VolID5*
> > > >
> > > > *1VolID6*
> > > >
> > > > *1ComptPhan*
> > > >
> > > > *1ComptDet*
> > > >
> > > > *1ReyPhan*
> > > >
> > > > *1ReyDet*
> > > >
> > > > *1ScannAx*
> > > >
> > > > *1ScannAng*
> > > >
> > > > *2IDRun*
> > > >
> > > > *2IDEvent*
> > > >
> > > > *2IDSource*
> > > >
> > > > *2AnihX*
> > > >
> > > > *2AnihY*
> > > >
> > > > *2AnihZ*
> > > >
> > > > *2TimeStamp*
> > > >
> > > > *2EnergyDep*
> > > >
> > > > *2EventX*
> > > >
> > > > *2EventY*
> > > >
> > > > *2EventZ*
> > > >
> > > > *2VolID1*
> > > >
> > > > *2VolID2*
> > > >
> > > > *2VolID3*
> > > >
> > > > *2VolID4*
> > > >
> > > > *2VolID5*
> > > >
> > > > *2VolID6*
> > > >
> > > > *2ComptPhan*
> > > >
> > > > *2ComptDet*
> > > >
> > > > *2ReyPhan*
> > > >
> > > > *2ReyDet*
> > > >
> > > > *2ScannAx*
> > > >
> > > > *2ScannAng*
> > > >
> > > > 0
> > > >
> > > > 154
> > > >
> > > > 0
> > > >
> > > > 5.18E+00
> > > >
> > > > -1.93E+00
> > > >
> > > > -1.74E+00
> > > >
> > > > 4.15E-05
> > > >
> > > > 4.99E-01
> > > >
> > > > 3.29E+01
> > > >
> > > > -5.39E+01
> > > >
> > > > 6.66E+00
> > > >
> > > > 0
> > > >
> > > > 3
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0.00E+00
> > > >
> > > > 0.00E+00
> > > >
> > > > 0
> > > >
> > > > 154
> > > >
> > > > 0
> > > >
> > > > 5.18E+00
> > > >
> > > > ########
> > > >
> > > > ########
> > > >
> > > > 4.15E-05
> > > >
> > > > 4.83E-01
> > > >
> > > > -2.97E+01
> > > >
> > > > 6.15E+01
> > > >
> > > > -1.29E+01
> > > >
> > > > 0
> > > >
> > > > 7
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0
> > > >
> > > > 0.00E+00
> > > >
> > > > 0.00E+00
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > I hope that helps. Surely format of two tables above is lost in
> > > > Gate list.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Marcin Balcerzyk,
> > > >
> > > > Unidad Ciclotron,
> > > >
> > > > Centro Nacional de Aceleradores,
> > > >
> > > > Universidad de Sevilla,
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Message: 3
> > > >
> > > > Date: Tue, 8 Feb 2011 15:18:04 +0100
> > > >
> > > > From: Nicolas GUIGNARD <nicolas.guignard8 at gmail.com>
> > > >
> > > > To: gate-users at lists.opengatecollaboration.org
> > > >
> > > > Subject: Re: [Gate-users] ASCII coincidence.dat analysis
> > > >
> > > > Message-ID:
> > > >
> > > > <AANLkTimG_2=swc-UpfEyFUkcCTuxmOiCuMWPqOam0p
> > > > +c at mail.gmail.com>
> > > >
> > > > Content-Type: text/plain; charset=ISO-8859-1
> > > >
> > > >
> > > >
> > > > Hello dear All
> > > >
> > > > I have seen lot of published literature using GATE and its
> > > > output
> > > > processing in forms of sinogram.That means persons using GATE
> > > > have procesed
> > > > the GATE ACSII files.But I am really so much surprised why
> > > > people don't
> > > > answer, share or guide how to do this for a naive user.
> > > >
> > > >
> > > >
> > > > Thanks
> > > >
> > > > Nicolas
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Gate-users mailing list
> > > Gate-users at lists.opengatecollaboration.org
> > > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > >
> > > End of Gate-users Digest, Vol 57, Issue 12
> > > ******************************************
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > 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
> http://www.imnc.in2p3.fr
> ----------------------------------------------------------------
>
>
>
>
More information about the Gate-users
mailing list