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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



----- Original Message -----
From: "Andreas Dräger" <andreas.draeger@uni-tuebingen.de>
To: <libsbml-discuss@caltech.edu>
Sent: Wednesday, June 21, 2006 3:43 PM
Subject: [libsbml-discuss] Problem with MatLab


> Hello,
>
> I am very new to SBML at all and thus having some questions how to get
> started. I used the CellDesigner to create a SBML file containing my
> model. Then I wanted to use this model in MatLab (with the SBToolbox).
> Therefore I followed the instructions to install both libsbml and also the
> SBToolbox successfully. When I tried the following in MatLab an error
> occured and I don't know how to solve this problem:
> ------------------------------------------------------------------------------------
> >> model = SBmodel('my_model.xml')
> ??? Undefined command/function 'TranslateSBML'.
>
> Error in ==> @SBmodel/private/SBimportSBML at 39
> SBMLmodel = TranslateSBML(SBMLmodelFile);
>
> Error in ==> SBmodel.SBmodel at 150
> [SBstructure,errorMsg] = SBimportSBML(filename);
>
> >>
> ------------------------------------------------------------------------------------
> I also tried to install the SBMLToolbox for MatLab. When I typed in "make"
> the following error occured:
> ------------------------------------------------------------------------------------
> [root@rapc77 toolbox]# make
> mex -I/usr/local/include -L/usr/local/lib TranslateSBML.c -lsbml
> TranslateSBML.c:61:30: xml/ParseMessage.h: No such file or directory
> TranslateSBML.c:62:23: util/util.h: No such file or directory
> TranslateSBML.c: In function `GetKineticLaw':
> TranslateSBML.c:1687: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetRule':
> TranslateSBML.c:2052: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetFunctionDefinition':
> TranslateSBML.c:2286: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetEvent':
> TranslateSBML.c:2409: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c:2414: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `GetEventAssignment':
> TranslateSBML.c:2564: warning: passing arg 1 of `LookForCSymbolTime'
> discards qualifiers from pointer target type
> TranslateSBML.c: In function `LookForCSymbolTime':
> TranslateSBML.c:2655: warning: assignment discards qualifiers from pointer
> target type
>
> mex: compile of 'TranslateSBML.c' failed.
>
> make: *** [TranslateSBML.mexglx] Error 1
> ------------------------------------------------------------------------------------
> Does anybody know, what to do?
>
> Thanks a lot for your help
> Andreas Dräger
>
> --
> Dipl.-Bioinform. Andreas Dräger
> Eberhard Karls University Tübingen
> Center for Bioinformatics (ZBIT)
> Phone: +49-7071-29-70436
> Fax: +49-7071-29-5091
>
>
>

Hello Andreas,
my quick and dirty solution for this problem:
CFLAGS="-I/usr/local/include -I/usr/local/include/sbml" make

/David Fange

On Thursday 22 June 2006 10:01, Andreas Dräger wrote:
> 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

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
>
>
>

Dear Sarah,

I just tried to use Matlab to import my SBML-model with the following
command line:

>> Model = TranslateSBML('my_model.xml')

Suddenly the Matlab window disappeared and in the terminal the following
error message occured:

*** glibc detected *** double free or corruption (out): 0xa9627968 ***

Seems that there is still something wrong.

With best regards
Andreas Dräger

--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Phone: +49-7071-29-70436
Fax: +49-7071-29-5091

Dear Sarah M. Keating,

I followed the discussion about the SBMLtoolbox on Matlab,
and tried the solutions posted by you and others.
As I know, there are two motifications proposed.

==============================================================

One is the "include section" of TranslateSBML.c
In my TranslateSBML.c, I have made it looks like ...

#include "sbml/SBMLReader.h"
#include "sbml/SBMLTypes.h"
#include "sbml/xml/ParseMessage.h"
#include "sbml/util/util.h"

==============================================================

Second way is the "variable defintion" of Makefile

MEX = /Applications/MATLAB704/bin/mex
XCFLAGS = $(CFLAGS)
XLDFLAGS = $(LDFLAGS) -L/usr/local/lib
XCPPFLAGS = $(CPPFLAGS) -I/usr/local/include -I/usr/local/include/sbml
LIBS = -lsbml

==============================================================

When I tried to "make" it, the message is shown as follows.


Applications/MATLAB704/bin/mex -I/usr/local/include -I/usr/local/include/sbml -L/usr/local/lib TranslateSBML.c -lsbml
TranslateSBML.c: In function `GetKineticLaw':
TranslateSBML.c:1686: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function `GetRule':
TranslateSBML.c:2051: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function `GetFunctionDefinition':
TranslateSBML.c:2285: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function `GetEvent':
TranslateSBML.c:2408: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c:2413: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function `GetEventAssignment':
TranslateSBML.c:2563: warning: passing arg 1 of `LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function `LookForCSymbolTime':
TranslateSBML.c:2654: warning: assignment discards qualifiers from pointer target type
ld: warning multiple definitions of symbol ___gxx_personality_v0
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_personality.o) private external definition of ___gxx_personality_v0 in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of ___gxx_personality_v0
ld: warning multiple definitions of symbol ___cxa_call_unexpected
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_personality.o) private external definition of ___cxa_call_unexpected in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of ___cxa_call_unexpected
ld: warning multiple definitions of symbol __ZTVSt9bad_alloc
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZTVSt9bad_alloc in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVSt9bad_alloc
ld: warning multiple definitions of symbol __ZNSt9bad_allocD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZNSt9bad_allocD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9bad_allocD2Ev
ld: warning multiple definitions of symbol __ZNSt9bad_allocD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZNSt9bad_allocD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9bad_allocD0Ev
ld: warning multiple definitions of symbol __ZSt15set_new_handlerPFvvE
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZSt15set_new_handlerPFvvE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt15set_new_handlerPFvvE
ld: warning multiple definitions of symbol __ZSt7nothrow
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZSt7nothrow in section (__TEXT,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt7nothrow
ld: warning multiple definitions of symbol __ZNSt9bad_allocD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(new_handler.o) private external definition of __ZNSt9bad_allocD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9bad_allocD1Ev
ld: warning multiple definitions of symbol __ZTVN10__cxxabiv121__vmi_class_type_infoE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVN10__cxxabiv121__vmi_class_type_infoE in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVN10__cxxabiv121__vmi_class_type_infoE
ld: warning multiple definitions of symbol __ZN10__cxxabiv117__class_type_infoD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv117__class_type_infoD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv117__class_type_infoD0Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv117__class_type_infoD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv117__class_type_infoD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv117__class_type_infoD1Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv117__class_type_infoD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv117__class_type_infoD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv117__class_type_infoD2Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv120__si_class_type_infoD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv120__si_class_type_infoD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv120__si_class_type_infoD0Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv120__si_class_type_infoD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv120__si_class_type_infoD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv120__si_class_type_infoD1Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv120__si_class_type_infoD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv120__si_class_type_infoD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv120__si_class_type_infoD2Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv121__vmi_class_type_infoD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv121__vmi_class_type_infoD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv121__vmi_class_type_infoD0Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv121__vmi_class_type_infoD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv121__vmi_class_type_infoD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv121__vmi_class_type_infoD1Ev
ld: warning multiple definitions of symbol __ZN10__cxxabiv121__vmi_class_type_infoD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZN10__cxxabiv121__vmi_class_type_infoD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZN10__cxxabiv121__vmi_class_type_infoD2Ev
ld: warning multiple definitions of symbol __ZNK10__cxxabiv117__class_type_info10__do_catchEPKSt9type_infoPPvj
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv117__class_type_info10__do_catchEPKSt9type_infoPPvj in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv117__class_type_info10__do_catchEPKSt9type_infoPPvj
ld: warning multiple definitions of symbol __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PKvRNS0_15__upcast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PKvRNS0_15__upcast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PKvRNS0_15__upcast_resultE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PPv
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PPv in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv117__class_type_info11__do_upcastEPKS0_PPv
ld: warning multiple definitions of symbol __ZNK10__cxxabiv117__class_type_info12__do_dyncastEiNS0_10__sub_kindEPKS0_PKvS3_S5_RNS0_16__dyncast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv117__class_type_info12__do_dyncastEiNS0_10__sub_kindEPKS0_PKvS3_S5_RNS0_16__dyncast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv117__class_type_info12__do_dyncastEiNS0_10__sub_kindEPKS0_PKvS3_S5_RNS0_16__dyncast_resultE
ld: warning multiple definitions of symbol __ZTVSt8bad_cast
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVSt8bad_cast in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVSt8bad_cast
ld: warning multiple definitions of symbol __ZTVSt10bad_typeid
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVSt10bad_typeid in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVSt10bad_typeid
ld: warning multiple definitions of symbol __ZNSt8bad_castD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt8bad_castD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt8bad_castD1Ev
ld: warning multiple definitions of symbol __ZNSt10bad_typeidD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt10bad_typeidD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt10bad_typeidD1Ev
ld: warning multiple definitions of symbol __ZNK10__cxxabiv117__class_type_info20__do_find_public_srcEiPKvPKS0_S2_
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv117__class_type_info20__do_find_public_srcEiPKvPKS0_S2_ in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv117__class_type_info20__do_find_public_srcEiPKvPKS0_S2_
ld: warning multiple definitions of symbol __ZTVN10__cxxabiv117__class_type_infoE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVN10__cxxabiv117__class_type_infoE in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVN10__cxxabiv117__class_type_infoE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv120__si_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv120__si_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv120__si_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE
ld: warning multiple definitions of symbol ___dynamic_cast
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of ___dynamic_cast in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of ___dynamic_cast
ld: warning multiple definitions of symbol __ZTVSt9type_info
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVSt9type_info in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVSt9type_info
ld: warning multiple definitions of symbol __ZNSt9type_infoD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt9type_infoD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9type_infoD2Ev
ld: warning multiple definitions of symbol __ZTVN10__cxxabiv120__si_class_type_infoE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZTVN10__cxxabiv120__si_class_type_infoE in section (__DATA,__const)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZTVN10__cxxabiv120__si_class_type_infoE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv120__si_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv120__si_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv120__si_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv120__si_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv120__si_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_ in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv120__si_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_
ld: warning multiple definitions of symbol __ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv121__vmi_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv121__vmi_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv121__vmi_class_type_info12__do_dyncastEiNS_17__class_type_info10__sub_kindEPKS1_PKvS4_S6_RNS1_16__dyncast_resultE
ld: warning multiple definitions of symbol __ZNK10__cxxabiv121__vmi_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNK10__cxxabiv121__vmi_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_ in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNK10__cxxabiv121__vmi_class_type_info20__do_find_public_srcEiPKvPKNS_17__class_type_infoES2_
ld: warning multiple definitions of symbol __ZNKSt9type_info10__do_catchEPKS_PPvj
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNKSt9type_info10__do_catchEPKS_PPvj in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNKSt9type_info10__do_catchEPKS_PPvj
ld: warning multiple definitions of symbol __ZNSt9type_infoD1Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt9type_infoD1Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9type_infoD1Ev
ld: warning multiple definitions of symbol __ZNSt9type_infoD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt9type_infoD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt9type_infoD0Ev
ld: warning multiple definitions of symbol __ZNSt8bad_castD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt8bad_castD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt8bad_castD2Ev
ld: warning multiple definitions of symbol __ZNSt8bad_castD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt8bad_castD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt8bad_castD0Ev
ld: warning multiple definitions of symbol __ZNSt10bad_typeidD2Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt10bad_typeidD2Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt10bad_typeidD2Ev
ld: warning multiple definitions of symbol __ZNSt10bad_typeidD0Ev
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNSt10bad_typeidD0Ev in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNSt10bad_typeidD0Ev
ld: warning multiple definitions of symbol __ZNKSt9type_info15__is_function_pEv
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNKSt9type_info15__is_function_pEv in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNKSt9type_info15__is_function_pEv
ld: warning multiple definitions of symbol __ZNKSt9type_info14__is_pointer_pEv
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNKSt9type_info14__is_pointer_pEv in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNKSt9type_info14__is_pointer_pEv
ld: warning multiple definitions of symbol __ZNKSt9type_info11__do_upcastEPKN10__cxxabiv117__class_type_infoEPPv
/usr/lib/gcc/darwin/3.3/libstdc++.a(tinfo.o) private external definition of __ZNKSt9type_info11__do_upcastEPKN10__cxxabiv117__class_type_infoEPPv in section (__TEXT,__text)
/usr/lib/libstdc++.6.dylib(single module) definition of __ZNKSt9type_info11__do_upcastEPKN10__cxxabiv117__class_type_infoEPPv
ld: multiple definitions of symbol __ZSt10unexpectedv
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt10unexpectedv
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_terminate.o) private external definition of __ZSt10unexpectedv in section (__TEXT,__text)
ld: multiple definitions of symbol __ZSt13set_terminatePFvvE
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt13set_terminatePFvvE
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_terminate.o) private external definition of __ZSt13set_terminatePFvvE in section (__TEXT,__text)
ld: multiple definitions of symbol __ZSt14set_unexpectedPFvvE
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt14set_unexpectedPFvvE
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_terminate.o) private external definition of __ZSt14set_unexpectedPFvvE in section (__TEXT,__text)
ld: multiple definitions of symbol __ZSt9terminatev
/usr/lib/libstdc++.6.dylib(single module) definition of __ZSt9terminatev
/usr/lib/gcc/darwin/3.3/libstdc++.a(eh_terminate.o) private external definition of __ZSt9terminatev in section (__TEXT,__text)

mex: link of 'TranslateSBML.mexmac' failed.

make: *** [TranslateSBML.mexglx] Error 1

===============================================================

My platform is MacOS 10.4, and I am sure that I've installed libsbml in proper location. Does it anything to do with the c complier on my machine?


Thank your patient to read it!

Sincerely

I am trying to build SBMLtoolbox (v.2.0.2) for Mac OSX (v.10.4.10). I am a novice Unix user; I know just enough to be dangerous, but not enough to debug the arcana of make files, etc.

I found that I needed to rearrange some of the directories in the SBMLtoolbox distribution; they seemed to be setup for a Win32 install, but not a Unix install. For instance, I needed to move /util and /xml directories from /win32/include/sbml to /toolbox in order to avoid a long litany of Unix "make" errors.

I still have a handful of errors remaining. They are all of the same nature:

====================================
mex -I/usr/local/include -I/usr/local/include -L/usr/local/lib -L/usr/local/lib TranslateSBML.c -lsbml
TranslateSBML.c: In function 'GetKineticLaw':
TranslateSBML.c:1687: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function 'GetRule':
TranslateSBML.c:2052: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function 'GetFunctionDefinition':
TranslateSBML.c:2286: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function 'GetEvent':
TranslateSBML.c:2409: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c:2414: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function 'GetEventAssignment':
TranslateSBML.c:2564: warning: passing argument 1 of 'LookForCSymbolTime' discards qualifiers from pointer target type
TranslateSBML.c: In function 'LookForCSymbolTime':
TranslateSBML.c:2655: warning: assignment discards qualifiers from pointer target type
/usr/bin/ld: can't locate file for: -lsbml
collect2: ld returned 1 exit status

mex: link of 'TranslateSBML.mexmaci' failed.

make: *** [TranslateSBML.mexmaci] Error 1
==========================================

I see that others have run across the same problem. And I see some confusing hacks about adding a second file path to the XCPPFLAGS environment variable (by the way, this did nothing for me, perhaps because there is no /usr/local/include/sbml directory on my disk). So the "fix" that might have worked for Andreas (it's confusing; first he posts "no more errors"; then he posts a long list of errors?!) doesn't work for me. Please help!

Sorry to bring this up again, but has this problem been solved?
I have been using sbml toolbox without output functions so far but now it would help me a lot if i can output the model as well.
is there anyone who installed sbmlToolbox without any errors on a mac? I would really want to know how they did it...

Thanks!

                                          
Emre Ozdemir

Hello friends

I've got a similar problem with SBMLToolbox-3.0.0, built in Ubuntu 9.10 64 bits, this time in OutputSBML.c:

mex -I/usr/local/include -I/usr/local/include/sbml -I/usr/local/include -L/usr/local/lib OutputSBML.c -lsbml
OutputSBML.c: In function ‘mexFunction’:
OutputSBML.c:220: warning: passing argument 1 of ‘SBase_setNotesString’ from incompatible pointer type

[...]

OutputSBML.c: In function ‘GetDelay’:
OutputSBML.c:4103: error: too few arguments to function ‘Delay_create’
OutputSBML.c:4116: warning: passing argument 1 of ‘SBase_setNotesString’ from incompatible pointer type
OutputSBML.c:4130: warning: passing argument 1 of ‘SBase_setAnnotationString’ from incompatible pointer type
OutputSBML.c:4144: warning: passing argument 1 of ‘SBase_setMetaId’ from incompatible pointer type
OutputSBML.c:4166: warning: passing argument 1 of ‘SBase_setSBOTerm’ from incompatible pointer type

mex: compile of ' "OutputSBML.c"' failed.


I tried all tweaks suggested here but none worked for me. Libsbl is correctly installed with --with-matlab option. Could you please help me?

Thanks a lot!

Javier