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Hi Andreas

This seems to be relating to the include structure; which has been an issue.

try replacing the line
XCPPFLAGS = $(CPPFLAGS) -I/usr/local/include

in the SBMLToolbox makefile with

XCPPFLAGS = $(CPPFLAGS) -I/usr/local/include -I/usr/local/include/sbml

which should then find the missing files.

I'm assuming you are building SBMLToolbox; or are you using the
libSBML --with-MATLAB

Sarah


----- Original Message -----
From: "Andreas Dräger" <andreas.draeger@uni-tuebingen.de>
To: "LibSBML Discussion List" <libsbml-discuss@caltech.edu>
Sent: Thursday, June 22, 2006 9:01 AM
Subject: Re: [libsbml-discuss] Problem with MatLab


> Hello Sarah,
>
> I still get an error message. However, the file common/extern.h and
> sbmlfwd.h does exist. What else could I change?
> Thank you a lot for your help!
>
> Andreas
>
> [root@rapc77 toolbox]# make
> mex -I/usr/local/include -L/usr/local/lib TranslateSBML.c -lsbml
> In file included from TranslateSBML.c:61:
> /usr/local/include/sbml/xml/ParseMessage.h:56:27: common/extern.h: No such
> file or directory
> /usr/local/include/sbml/xml/ParseMessage.h:156:28: common/sbmlfwd.h: No
> such file or directory
> TranslateSBML.c: In function `GetKineticLaw':
> TranslateSBML.c:1689: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetRule':
> TranslateSBML.c:2054: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetFunctionDefinition':
> TranslateSBML.c:2288: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetEvent':
> TranslateSBML.c:2411: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c:2416: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetEventAssignment':
> TranslateSBML.c:2566: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `LookForCSymbolTime':
> TranslateSBML.c:2657: warning: assignment discards qualifiers from pointer
> target type
>
> mex: compile of 'TranslateSBML.c' failed.
>
> make: *** [TranslateSBML.mexglx] Error 1
>
>
> Sarah Keating wrote:
>
>> Hi Andreas
>>
>> The build problem in SBMLToolbox is a bug in TranslateSBML.c - my fault
>> as I'm a windows user :-)
>>
>> If you change the includes at the top of TranslateSBML.c to read
>>
>> #include "sbml/xml/ParseMessage.h"
>> #include "sbml/util/util.h"
>> that should sort it! Once you have built TranslateSBML from SBMLToolbox
>> or libSBML SBToolbox should be fine.
>>
>> Remember to add the directory where TranslateSBML.mexglx is to your path
>> in MATLAB. Your initial problem could have been caused by this!
>>
>> Hope this helps
>>
>> Sarah
>
> --
> Dipl.-Bioinform. Andreas Dräger
> Eberhard Karls University Tübingen
> Center for Bioinformatics (ZBIT)
> Phone: +49-7071-29-70436
> Fax: +49-7071-29-5091
>
>
>