[Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11

[Dendooven Peter]

Hello,

as far as I remember, I downloaded the following:

	root_v5.22.00.macosx-i386-gcc-4.0.tar.gz

which as far as I understand is a binary (is that the same as what  
you mean with pre-compiled version ?). I do not remember doing any  
installation.

I notice the file has -i386 in it's name, whereas the error message I  
received contains -i686. Maybe there is a version incompatibility ?

Anyway, after discussing with my colleague who compiled ROOT himself  
(on Linux), I also did this. To try to be on the safe side, I  
installed the ROOT version which is just older than the release date  
of gate4.0.0, i.e. root 5.20. ROOT runs fine (it at least starts up  
OK, I haven't tried to make it perform any tasks).

When compiling GATE, the error messages related to files expected to  
be in /Users/brun/root/lib/ are gone. It seems that the pre-compiled  
version assumed the same installation locations as used by Rene Brun,  
one of the main ROOT developers...

Now compiling GATE again using the same procedure as I described  
earlier still gives the following:
	i686-apple-darwin8-g++-4.0.1: unrecognized option '-rdynamic'
followed by:
	/usr/bin/ld: Undefined symbols:
	TFile::TFile(char const*, char const*, char const*, int)
	ROOT::Math::RootFinder::RootFinder(ROOT::Math::RootFinder::EType)
	ROOT::Math::RootFinder::~RootFinder()
	...(many more lines)

The final 2 lines are:
	collect2: ld returned 1 exit status
	make: *** [bin/Darwin-g++/Gate] Error 1
after which the process terminates without the Gate executable being  
created.

Attached the whole make.log file.

There seems to be slow progress, but I feel I'm still installing  
incompatible versions of certain software. I hope someone has more  
suggestions of what might be wrong.

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Cheers,
Peter


On 19 Jun 2009, at 10:46, THIAM Cheick 219838 wrote:

> Hello Peter,
>
> My feeling is that your problem comes from ROOT installation...  
> Have you installed ROOT using a code source or pre-compiled version  
> for Mac?
>
> I think that things lack in root libraries list in your  
> installation... So I suggest you use a pre-compiled version for Mac- 
> OS 10.4 on ROOTSYS web site
>
> May be it will work's this time
>
> Let me know
> Cheick
>
>
> -----Message d'origine-----
> De : Dendooven Peter [mailto:dendooven at kvi.nl]
> Envoy? : jeudi 18 juin 2009 16:59
> ? : THIAM Cheick 219838
> Cc : gate-users at lists.healthgrid.org
> Objet : Re: [Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11
>
> Below the procedure I follow. This is partially based on input from a
> colleague running GATE under Linux.
>
> 1) Open "Terminal" application to start with a fresh terminal window.
>
> 2) Go to the GATE directory: /Applications/gate_v4.0.0
>
> 3) set the following environment variables (given are the values
> confirmed by echo):
>
> ROOTSYS = /Applications/root
> G4INSTALL = /Applications/geant4.9.1.p03
> G4WORKDIR = /Applications/g4work
> G4VERSION = 9.1
> GATEHOME = /Applications/gate_v4.0.0
> PATH = /sw/bin:/sw/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/
> usr/texbin:/usr/X11R6/bin:/Applications/root/bin:/Applications/root/
> lib:/Applications/root/include:/Applications/gate_v4.0.0/bin/Darwin-g+
> +:/Applications/g4work/bin/Darwin-g++:/Applications/g4work/bin/Darwin-
> g++:/Applications/root/bin:/Applications/root/lib:/Applications/root/
> include:/Applications/gate_v4.0.0/bin/Darwin-g++
> LD_LIBRARY_PATH = /Applications/root/lib
> DYLD_LIBRARY_PATH = /Applications/root/lib
>
> 4) Launching GATE configuration script /Applications/gate_v4.0.0/
> env_gate.csh
>
> This produces the following output, of which the first part comes
> from the geant configuration script:
>
> The current value of G4INSTALL is: /Applications/geant4.9.1.p03
> The current value of G4VERSION is: 9.1
>
> Launching Geant4 configuration script /Applications/geant4.9.1.p03/
> env.csh
>
> On this machine the G4SYSTEM=Darwin-g++
> On this machine the G4INSTALL=/Applications/geant4.9.1.p03
> On this machine the G4LIB=/Applications/geant4.9.1.p03/lib
> On this machine the G4LEVELGAMMADATA=/Applications/geant4.9.1.p03/
> data/PhotonEvaporation2.0
> On this machine the G4RADIOACTIVEDATA=/Applications/geant4.9.1.p03/
> data/RadioactiveDecay3.2
> On this machine the G4LEDATA=/Applications/geant4.9.1.p03/data/
> G4EMLOW5.1
> On this machine the G4NEUTRONHPDATA=/Applications/geant4.9.1.p03/data/
> G4NDL3.12
> On this machine the G4ABLADATA=/Applications/geant4.9.1.p03/data/
> G4ABLA3.0
> On this machine the CLHEP_BASE_DIR=/Applications/CLHEP
> On this machine the CLHEP_INCLUDE_DIR=/Applications/CLHEP/include
> On this machine the CLHEP_LIB_DIR=/Applications/CLHEP/lib
> On this machine the CLHEP_LIB=CLHEP
> On this machine the G4VIS_BUILD_OPENGLX_DRIVER=1
> On this machine the G4VIS_BUILD_RAYTRACERX_DRIVER=1
> On this machine the G4VIS_USE_OPENGLX=1
> On this machine the G4VIS_USE_RAYTRACERX=1
> On this machine the XMFLAGS=
> On this machine the XMLIBS=
> On this machine the XMFLAGS=
> On this machine the XMLIBS=
> 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
> On this machine the G4UI_USE_TCSH=1
> In your environment you have the G4WORKDIR=/Applications/g4work
>
> 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 enabled
> Checking your LD_LIBRARY_PATH variable...
>   ==> OK: /Applications/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 /Applications/gate_v4.0.0
> Checking your path variable...
>   ==> OK: /Applications/gate_v4.0.0/bin/Darwin-g++ is already in your
> path variable
> GATEHOME = /Applications/gate_v4.0.0
> G4VERSION9 is set: GATE is compatible with the geant4 version 9.1
>
> Done
>
> 5) Making sure there is no /tmp or /bin directory in the GATEHOME
> directory.
>
> 6) Give the following command:
>
> make >&make.log
>
> The make.log file is attached.
>
> All seems to go well up to:
>
> Compiling Gate.cc ...
> Using granular libraries ...
> Linking Gate ...
> i686-apple-darwin8-g++-4.0.1: unrecognized option '-rdynamic'
> /usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
> libMathCore.dylib referenced from: /Applications/root/lib/
> libHist.dylib (checking for undefined symbols may be affected) (No
> such file or directory, errno = 2)
> /usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
> libRIO.dylib referenced from: /Applications/root/lib/libGraf.dylib
> (checking for undefined symbols may be affected) (No such file or
> directory, errno = 2)
> /usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
> libNet.dylib referenced from: /Applications/root/lib/libTree.dylib
> (checking for undefined symbols may be affected) (No such file or
> directory, errno = 2)
> /usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
> libThread.dylib referenced from: /Applications/root/lib/libTree.dylib
> (checking for undefined symbols may be affected) (No such file or
> directory, errno = 2)
> /usr/bin/ld: Undefined symbols:
> TFile::TFile(char const*, char const*, char const*, int)
> TVirtualFitter::GetFitter()      referenced from libHist expected to
> be defined in /Users/brun/root/lib/libMathCore.dylib
> TVirtualFitter::SetFitter(TVirtualFitter*, int)referenced from
> libHist expected to be defined in /Users/brun/root/lib/ 
> libMathCore.dylib
> ROOT::Fit::Fitter::SetFunction
> (ROOT::Math::IParametricFunctionMultiDim const&)referenced from
> libHist expected to be defined in /Users/brun/root/lib/ 
> libMathCore.dylib
> ROOT::Fit::Fitter::SetFunction
> (ROOT::Math::IParametricGradFunctionOneDim const&)referenced from
> libHist expected to be defined in /Users/brun/root/lib/ 
> libMathCore.dylib
>
> (a long list of similar messages follows, ending with:)
>
> TSQLRow::ShowMembers(TMemberInspector&, char*)  referenced from
> libTree expected to be defined in /Users/brun/root/lib/libNet.dylib
> collect2: ld returned 1 exit status
> make: *** [bin/Darwin-g++/Gate] Error 1
>
> So a lot of things are not where they are expected or are expected in
> directories that do not exist (such as /Users/brun).
> Also, i686-apple-darwin8-g++-4.0. is asked to do something is does
> not recognize.
>
> At this point, echo $DYLD_LIBRARY_PATH gives:
> /Applications/root/lib
>
> I hope this information helps.
>
> Cheers,
> Peter
>