<html><head><style type="text/css"></style></head><body><div style="font-family:Courier New,courier,monaco,monospace,sans-serif;font-size:10pt"><div>Hello, first, </gate/output/ascii/setOutFileSinglesFlag 0> cannot work until </gate/digitizer/Singles/insert adder> do. second, I use Geant 4.9.p01 (28-08-2007) as recommended, not 4.9.p02. For me it work with 4.9.p01 (if I remember it also work for me with 4.8.p02) </div><div style="font-family: Courier New,courier,monaco,monospace,sans-serif; font-size: 10pt;"> Best regards, Samuel Burg <div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;">----- Message d'origine ---- De : franklin pereira <pnicholasf@gmail.com> À : Samuel BURG <samuel_burg@yahoo.fr> Envoyé le : Lundi, 28 Juillet 2008, 20h54mn 37s Objet : Re: Re : [Gate-users] Problems with compiling GATE Hello, I installed root-5.14, recompiled geant and gate using gcc-4.1.2 After that I tried the PET benchmark tests but it aborts. I have included the std output here. As you will notice, the commands that do not execute are: ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> ***** ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesFlag 0> ***** Also, I set the flags for graphics output using openGL, but this does not show in the available graphics system list detected by gate. I checked for openGL libraries and they are there ( they come with the ubuntu 8.04 distribution). Also the geant configure script is able to detect it under the /usr directory. I'd appreciate your feedback in this regard. Thank you, Franklin. ************************************************************* Geant4 version Name: geant4-09-00-patch-02    (25-January-2008)                       Copyright : Geant4 Collaboration                       Reference : NIM A 506 (2003), 250-303                             WWW : <a href="http://cern.ch/geant4" target="_blank">http://cern.ch/geant4</a> ************************************************************* Visualization Manager instantiating... Visualization Manager initialising... Registering graphics systems... You have successfully registered the following graphics systems. Current available graphics systems are:   ASCIITree (ATree)   DAWNFILE (DAWNFILE)   G4HepRep (HepRepXML)   G4HepRepFile (HepRepFile)   RayTracer (RayTracer)   VRML1FILE (VRML1FILE)   VRML2FILE (VRML2FILE) Registering model factories... You have successfully registered the following model factories. Registered model factories:   generic   drawByCharge   drawByParticleID   drawByOriginVolume   drawByAttribute Registered filter factories:   chargeFilter   particleFilter   originVolumeFilter   attributeFilter Time set to (s) 0 [GateSystemListManager::CheckScannerAutoCreation:     Creating new system based on volume inserter 'cylindricalPET' GATE object:        'systems/cylindricalPET' Components: GATE object:        'systems/cylindricalPET/base' Attached to volume: cylindricalPET Nb of children:      1     GATE object:        'systems/cylindricalPET/rsector'     Attached to volume: head     Nb of children:      1         GATE object:        'systems/cylindricalPET/module'         Attached to volume: module         Nb of children:      1             GATE object:        'systems/cylindricalPET/submodule'             Attached to volume: block             Nb of children:      1                 GATE object:        'systems/cylindricalPET/crystal'                 Attached to volume: crystal                 Nb of children:      4                     GATE object:        'systems/cylindricalPET/layer0'                     Attached to volume: LSO                     Nb of children:      0                     GATE object:        'systems/cylindricalPET/layer1'                     Attached to volume: BGO                     Nb of children:      0                     GATE object:        'systems/cylindricalPET/layer2'                     Attached to volume: ---                     Nb of children:      0                     GATE object:        'systems/cylindricalPET/layer3'                     Attached to volume: ---                     Nb of children:      0 geometrical design type: 1 ring diameter: 86.5 cm rsector axial pitch: 0 fm rsector azimuthal pitch: 45 degree rsector tangential size: 32 cm rsector axial size: 40.2 cm module axial size: 10 cm module tangential size: 8 cm module axial pitch: 10 cm module tangential pitch: 8 cm submodule axial size: 1.99 cm submodule tangential size: 1.59 cm submodule axial pitch: 2 cm submodule tangential pitch: 1.6 cm crystal radial size: 3 cm crystal axial size: 3.8 mm crystal tangential size: 3 mm crystal axial pitch: 4 mm crystal tangential pitch: 3.2 mm layer0 radial size: 1.5 cm in layer0 interaction length: 7.5 mm layer1 radial size: 1.5 cm in layer1 interaction length: 7.5 mm Axial nb of rsectors: 1 Azimuthal nb of rsectors: 8 Axial nb of modules: 4 Tangential nb of modules: 4 Axial nb of submodules: 5 Tangential nb of submodules: 5 Axial nb of crystals: 5 Tangential nb of crystals: 5 Radial nb of layers: 2 WARNING ! SetCutValueForOthers became obsolete. It is harmless to remove this invokation without any side effects. This dummy method implementation will be removed soon. ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> ***** ***** Batch is interupted!! ***** Ignoring confine condition Ignoring confine condition GateSourceMgr::ListSources: List of the sources in the source managaer Source --------------> F18LineSource   ID                : 0   type              :   activity (Bq)      : 100000   startTime (s)      : 0   time (s)          : 0   forcedUnstable    : 1   forcedHalfLife (s) : 6586.2   verboseLevel      : 0 ---------------------- Source --------------> O15LineSource   ID                : 1   type              :   activity (Bq)      : 100000   startTime (s)      : 0   time (s)          : 0   forcedUnstable    : 1   forcedHalfLife (s) : 122.24   verboseLevel      : 0 ---------------------- ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesFlag 0> ***** ***** Batch is interupted!! ***** Graphics systems deleted. Visualization Manager deleting... 2008/7/28 Samuel BURG <<a ymailto="mailto:samuel_burg@yahoo.fr" href="mailto:samuel_burg@yahoo.fr">samuel_burg@yahoo.fr</a>>: > > The best solution is to downgarde GCC to 4.1.x. > Then you can compil all the stuff for Gate without any error. > It's better to use ROOT 5.14 for Gate 3.1.2 > > I've allready do that on Ubuntu 8.04 TSL x64, so I know the relevent > packadges are availaible. > > Best regards, > > Samuel Burg > > > ----- Message d'origine ---- > De : Zhibin Huang <<a ymailto="mailto:zxh6@case.edu" href="mailto:zxh6@case.edu">zxh6@case.edu</a>> > À : franklin pereira <<a ymailto="mailto:pnicholasf@gmail.com" href="mailto:pnicholasf@gmail.com">pnicholasf@gmail.com</a>> > Cc : <a ymailto="mailto:gate-users@lists.healthgrid.org" href="mailto:gate-users@lists.healthgrid.org">gate-users@lists.healthgrid.org</a> > Envoyé le : Vendredi, 25 Juillet 2008, 21h06mn 36s > Objet : Re: [Gate-users] Problems with compiling GATE > > Recently I successfully installed Gate under Ubuntu8.04 when I used > ROOT5.19. It seems that in Ubntu8.04, ROOT5.14 can't be compiled > successfully. > > Before you install GATE, you have to modify the GNUmake file. As a > reference, please see the attachment and modify the path properly. My > webpage may also be useful for both Gate installation and Ubuntu8.04 > configuration: > please search for GATE under the link: > <a href="https://filer.case.edu/%7Ezxh6/data/daily-log" target="_blank">https://filer.case.edu/~zxh6/data/daily-log</a> > > Good luck! > > On Fri, Jul 25, 2008 at 1:43 PM, franklin pereira <<a ymailto="mailto:pnicholasf@gmail.com" href="mailto:pnicholasf@gmail.com">pnicholasf@gmail.com</a>> > wrote: >> >> Hi, >> >> I have a Dell Vostro ( intel core duo processor) with Ubuntu 8.04 >> installed. >> The default version of the gcc compiler is 4.2.3 >> >> I recently downloaded Gate3.1.2, Geant4 (version 9.0), ROOT (5.14). >> >> Geant4 compiled without any problems. >> >> However, I am having problems with compiling ROOT-5.14. >> I get tons of warnings and then the compilation aborts with the >> following error message: >> >> >> ************************************************************************************************************************* >> >>  bin/rmkdepend -R -fcint/src/gcc3strm.d -Y -w 1000 -- -pipe -m32 -Wall >> >> -W -Woverloaded-virtual -fPIC -Iinclude  -DG__REGEXP -DG__UNIX >> >> -DG__SHAREDLIB -DG__OSFDLL -DG__ROOT -DG__REDIRECTIO -DG__STD_EXCEPTION >> >> -DG__HAVE_CONFIG -DG__NOMAKEINFO -DG__CINTBODY -Icint/src -pthread >> >> -Icint/lib/gcc3strm -D__cplusplus -- cint/src/gcc3strm.cxx >> g++ -O  -pipe -m32 -Wall -W -Woverloaded-virtual -fPIC -Iinclude >> -DG__REGEXP -DG__UNIX -DG__SHAREDLIB -DG__OSFDLL -DG__ROOT >> -DG__REDIRECTIO -DG__STD_EXCEPTION -DG__HAVE_CONFIG -DG__NOMAKEINFO >> -DG__CINTBODY -Icint/src -pthread -Icint/lib/gcc3strm -o >> cint/src/gcc3strm.o -c cint/src/gcc3strm.cxx >> cint/src/gcc3strm.cxx: In function 'int G__G__stream_7_7_0(G__value*, >> const char*, G__param*, int)': >> cint/src/gcc3strm.cxx:311: error: 'class std::fpos<__mbstate_t>' has >> no member named 'operator==' >> cint/src/gcc3strm.cxx: In function 'int G__G__stream_7_8_0(G__value*, >> const char*, G__param*, int)': >> cint/src/gcc3strm.cxx:317: error: 'class std::fpos<__mbstate_t>' has >> no member named 'operator!=' >> make: *** [cint/src/gcc3strm.o] Error 1 >> >> ************************************************************************************************************************* >> >> >> ROOT 5.20, however, compiles cleanly, but gate will not compile with >> this version of ROOT as is cannot find the proper function >> declarations for the various ROOT functions ( the header files are in >> /root/include and this is passed on to the g++ compiler correctly >> in the GATE makefile ). >> >> >> A sample of these error messages are: >> >> >> ************************************************************************************************************** >> >>Using global libraries ... >> Linking Gate ... >> >> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateHitFileReader.o): >> In function `GateHitFileReader::PrepareAcquisition()': >> GateHitFileReader.cc:(.text+0x102a): undefined reference to >> `TFile::TFile(char const*, char const*, char const*, int)' >> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o): >> In function `GateToRoot::RecordVoxels(GateVGeometryVoxelStore*)': >> GateToRoot.cc:(.text+0xe47): undefined reference to `TFile::TFile(char >> const*, char const*, char const*, int)' >> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o): >> In function `GateToRoot::RecordBeginOfAcquisition()': >> GateToRoot.cc:(.text+0x3fd3): undefined reference to >> `TFile::TFile(char const*, char const*, char const*, int)' >> GateToRoot.cc:(.text+0x423b): undefined reference to >> `TFile::TFile(char const*, char const*, char const*, int)' >> /opt/root/lib/libTree.so: undefined reference to >> `TFileCacheRead::TFileCacheRead(TFile*, int)' >> /opt/root/lib/libTree.so: undefined reference to `TFile::GetCacheRead() >> const' >> /opt/root/lib/libTree.so: undefined reference to >> `TBufferFile::WriteClones(TClonesArray*, int)' >> /opt/root/lib/libTree.so: undefined reference to >> `TBufferFile::WriteArray(float const*, int)' >> /opt/root/lib/libTree.so: undefined reference to >> `TSQLRow::Streamer(TBuffer&)' >> /opt/root/lib/libTree.so: undefined reference to >> `TBufferFile::WriteVersion(TClass const*, bool)' >> /opt/root/lib/libHist.so: undefined reference to >> `ROOT::Fit::BinData::Initialize(unsigned int, unsigned int, >> ROOT::Fit::BinData::ErrorType)' >> /opt/root/lib/libTree.so: undefined reference to `typeinfo for TSQLResult' >> /opt/root/lib/libTree.so: undefined reference to >> `TBufferFile::ReadObject(TClass const*)' >> /opt/root/lib/libTree.so: undefined reference to `TKey::Create(int, >> TFile*)' >> >> ******************************************************************************************************************** >> >> >> My guess is that the function declarations in ROOT5.20 have changed >> from version 5.14, therefore the conflict. >> However, I am clueless regarding the compilation errors generated >> while trying to compile ROOT-5.14. >> Is this due to the newer version of gcc that comes with the Ubuntu OS >> ? I am at a loss and would appreciate help regarding this. >> >> Thanks a lot, >> Franklin. >> _______________________________________________ >> Gate-users mailing list >> <a ymailto="mailto:Gate-users@lists.healthgrid.org" href="mailto:Gate-users@lists.healthgrid.org">Gate-users@lists.healthgrid.org</a> >> <a href="http://lists.healthgrid.org/mailman/listinfo/gate-users" target="_blank">http://lists.healthgrid.org/mailman/listinfo/gate-users</a> > > > ________________________________ > Envoyé avec Yahoo! Mail. > Une boite mail plus intelligente. > _______________________________________________ > Gate-users mailing list > <a ymailto="mailto:Gate-users@lists.healthgrid.org" href="mailto:Gate-users@lists.healthgrid.org">Gate-users@lists.healthgrid.org</a> > <a href="http://lists.healthgrid.org/mailman/listinfo/gate-users" target="_blank">http://lists.healthgrid.org/mailman/listinfo/gate-users</a> > > </div></div></div> <hr size="1"> Envoyé avec <a href="http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52423/*http://fr.docs.yahoo.com/mail/overview/index.html">Yahoo! Mail</a>. Une boite mail plus intelligente. </a></body></html>