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

[Rainer M. <ra...@tb...>]

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
>>>>>
>>>>
>>>
>>
>