Re: [SOSlib-devel] building SBML ODE Solver for AIX - can I use expat?[Scanned]

[Christoph F. <xt...@tb...>]

hi rainer, andrew,

yes some of the libsbml versions need the
-I/hpc/home/finneya/programs/include/sbml added to the CFLAGS.

you can remove the -rpath from the LDFLAGS and put the specified paths
into your LD_LIBRARY_PATH variable, so that the shared libraries are
found at runtime.

=;) xtof

Rainer Machne writes:
 > Andrew
 > 
 > On Thu, 8 Jun 2006, Andrew Finney wrote:
 > 
 > > This is a not so recent version of 1.6.0
 > 
 > If it's not the official release version, then it might be missing
 > included the work-around for libSBML version inconsistencies.
 > 
 > Your CFLAGS where
 > 
 > >>  CFLAGS=-g -O2 -I/hpc/home/finneya/programs/include
 > 
 > The latest version of the configure process two values for the include 
 > path for libSBML. 
 > The second value in your case would be
 > 
 >   -I/hpc/home/finneya/programs/include/sbml
 > 
 > I think this was necessary because of different structuring of the header 
 > files in different libSBML versions. Is this correct, Christoph?
 > 
 > You could try to add the second path to the CFLAGS or just use the 
 > official release version.
 > 
 > Rainer
 > 
 > >
 > > Andrew
 > >> -----Original Message-----
 > >> From: Rainer Machne [mailto:ra...@tb...]
 > >> Sent: 08 June 2006 15:25
 > >> To: Andrew Finney; Christoph Flamm
 > >> Cc: SOSlib Development
 > >> Subject: Re: [SOSlib-devel] building SBML ODE Solver for AIX
 > >> - can I use expat?[Scanned]
 > >>
 > >>
 > >>>
 > >>> It looks as if the loader (ld) isn't performing as expected :-(
 > >>>
 > >>> what's the -rpath supposed to do?
 > >>
 > >>
 > >> Maybe Xtof can help out here.
 > >>
 > >> Just a short question: are you trying to compile version
 > >> 1.5.0 or is there an old version number hidden somewhere in
 > >> the configure process?
 > >>
 > >> Rainer
 > >>
 > >> On Thu, 8 Jun 2006, Andrew Finney wrote:
 > >>
 > >>> Rainer
 > >>>
 > >>> I managed to substitute expat for xerces
 > >>>
 > >>> But I still can't link to libsbml in the config.log
 > >>> (attached)
 > >>> I get the following:
 > >>>
 > >>> ---------------------------------
 > >>>
 > >>> configure:4155: checking correct functioning of SBML
 > >>> configure:4185: gcc -o conftest -g -O2
 > >>> -I/hpc/home/finneya/programs/include
 > >>> -Wl,-rpath,/hpc/home/finneya/programs/lib
 > >>> -L/hpc/home/finneya/programs/lib conftest.c  -lexpat -lsbml >&5
 > >>> ld: 0706-012 The -p flag is not recognized.
 > >>> ld: 0706-012 The -a flag is not recognized.
 > >>> ld: 0706-012 The -t flag is not recognized.
 > >>> ld: 0706-012 The -h flag is not recognized.
 > >>> collect2: ld returned 255 exit status
 > >>> configure:4191: $? = 1
 > >>> configure: failed program was:
 > >>> | /* confdefs.h.  */
 > >>> |
 > >>> | #define PACKAGE_NAME "odeSolver"
 > >>> | #define PACKAGE_TARNAME "SBML_odeSolver"
 > >>> | #define PACKAGE_VERSION "1.5.0"
 > >>> | #define PACKAGE_STRING "odeSolver 1.5.0"
 > >>> | #define PACKAGE_BUGREPORT "{raim,xtof}@tbi.univie.ac.at"
 > >>> | #define PACKAGE "SBML_odeSolver"
 > >>> | #define VERSION "1.5.0"
 > >>> | #ifdef __cplusplus
 > >>> | extern "C" void std::exit (int) throw (); using std::exit; #endif
 > >>> | /* end confdefs.h.  */
 > >>> | #include <sbml/SBMLTypes.h>
 > >>> | int
 > >>> | main ()
 > >>> | {
 > >>> | SBMLReader_t *sr; sr = SBMLReader_create(); SBMLReader_free(sr);
 > >>> |   ;
 > >>> |   return 0;
 > >>> | }
 > >>> configure:4220: result: no:
 > >>>                   CFLAGS=-g -O2 -I/hpc/home/finneya/programs/include
 > >>>                   LDFLAGS= -Wl,-rpath,/hpc/home/finneya/programs/lib
 > >>> -L/hpc/home/finneya/programs/lib
 > >>>                   LIBS= -lexpat -lsbml
 > >>> configure:4228: error: Can not link to SBML Library:
 > >>> 		  Please, make sure to use libSBML version >= 2.3.2
 > >>>
 > >>> ------------------
 > >>>
 > >>> It looks as if the loader (ld) isn't performing as expected :-(
 > >>>
 > >>> what's the -rpath supposed to do?
 > >>>
 > >>> yours Andrew
 > >>>
 > >>>
 > >>>> -----Original Message-----
 > >>>> From: Rainer Machne [mailto:ra...@tb...]
 > >>>> Sent: 08 June 2006 14:13
 > >>>> To: Andrew Finney
 > >>>> Cc: SOSlib Development
 > >>>> Subject: Re: building SBML ODE Solver for AIX - can I use
 > >>>> expat?[Scanned]
 > >>>>
 > >>>> Hi Andrew
 > >>>>
 > >>>> Unfortunately we completely forgot about libSBML with expat.
 > >>>>
 > >>>> There is a bug report in sourceforge with short instructions.
 > >>>> http://sourceforge.net/tracker/index.php?func=detail&aid=14204
 > >>>> 89&group_id=139893&atid=744811
 > >>>>
 > >>>>
 > >>>> Copied from there, with slight corrections:
 > >>>>
 > >>>> This bug can temporarily be solved simply by replacing all
 > >> occurences
 > >>>> of
 > >>>>
 > >>>> `-lxerces-c'
 > >>>>
 > >>>> in the files:
 > >>>>
 > >>>> configure
 > >>>> src/Makefile.am
 > >>>> src/Makefile.in
 > >>>> examples/Makefile.am
 > >>>> examples/Makefile.in
 > >>>> odeSolver/Makefile.am
 > >>>> odeSolver/Makefile.in
 > >>>>
 > >>>> with `-lexpat'
 > >>>>
 > >>>> e.g. by usind sed:
 > >>>>
 > >>>> sed 's/xerces-c/expat/g' configure >configure.new mv configure.new
 > >>>> configure
 > >>>>
 > >>>> for all above files.
 > >>>>
 > >>>>
 > >>>> I tried it once and it worked! Please let me know if you suceed!
 > >>>>
 > >>>> Rainer
 > >>>>
 > >>>>
 > >>>>
 > >>>> On Thu, 8 Jun 2006, Andrew Finney wrote:
 > >>>>
 > >>>>> Rainer
 > >>>>>
 > >>>>> I'm trying to build SOS on AIX
 > >>>>>
 > >>>>> for some reason I'm having problems linking with xerces for that
 > >>>>> platform
 > >>>>>
 > >>>>> Is there a way to configure SOS to use expat?
 > >>>>>
 > >>>>> Andrew
 > >>>>>
 > >>>>
 > >>>
 > >>
 > >
 > 
 > 
 > _______________________________________________
 > sbmlsolver-devel mailing list
 > sbm...@li...
 > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel

-- 
Christoph Flamm
Bioinformatik, Inst.f.Informatik, Univ.Leipzig, Germany
  www: http://www.tbi.univie.ac.at/~xtof
phone: ++49 341 97-16688 fax: ++49 341 97-16709
email: xt...@bi...
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