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Hello Celine,

I'm sorry you encountered problems with the Matlab bindings on Linux. It is
a difficult platform to support with its variety. So thank you first of all
for letting us know and we will make sure that the compilation gets easier
going forward. Let me turn to your actual issue:

>
> Warning: You are using gcc version "4.4.4-14ubuntu5)". The version
> currently supported with MEX is "4.3.4".
> For a list of currently supported compilers see:
> http://www.mathworks.com/support/compilers/current_release/

This warning is issued by the Matlab compilation script, and can in fact be
disregarded. The newest gcc will work just fine with the Matlab bindings.

However, unfortunately both the script seems to work differently on Linux
than it does on OSX. So to compile the Matlab bindings minor tweaks have to
be made:

For libsbml 4.1.0 and 4.2.0 please edit the src/bindings/matlab/Makefile.in
file and replace:


%.$(MEXEXT): %.c
env MATLABROOT=$(MATLABROOT) ARCH=$(MEX_ARCH) Arch=$(MEX_ARCH) \
CFLAGS="${CFLAGS}" $(LIBTOOL) --tag=CC --mode=link $(MEX) \
ARCH=$(MEX_ARCH) Arch=$(MEX_ARCH) -f $(mexopts_file) \
-o $@ $^ $(flags) ../../libsbml.la $(MATLAB_LIBS)
cp -f .libs/$@ .

with:


%.$(MEXEXT): %.c
env MATLABROOT=$(MATLABROOT) ARCH=$(MEX_ARCH) Arch=$(MEX_ARCH) \
CFLAGS="${CFLAGS}" $(LIBTOOL) --tag=CC --mode=link $(MEX) \
ARCH=$(MEX_ARCH) Arch=$(MEX_ARCH) -f ./$(mexopts_file) \
-o $@ $^ $(flags) ../../libsbml.la $(MATLAB_LIBS)
cp -f .libs/$@ .

(note the ./ in front of $(mexopts_file) ).

For libsbml 5.0.0-b1, please edit the file
src/common/operationReturnValues.h and replace:


//--------------------------------------------------------------------------
-
//
// Return codes for package extension
//

//--------------------------------------------------------------------------
-

with

/*
---------------------------------------------------------------------------
*
* Return codes for package extension
*
*
--------------------------------------------------------------------------
*/

After making these changes running the configure script again will resolve
the issues.

All these changes are in SVN and will be in the next libsbml release.

Sorry for the inconvenience, please let us know if you have further problems

Best
Frank



> -----Original Message-----
> From: sbml-interoperability-bounces@caltech.edu [mailto:sbml-
> interoperability-bounces@caltech.edu] On Behalf Of celine
> Sent: Wednesday, January 26, 2011 1:22 PM
> To: sbml-interoperability@caltech.edu
> Subject: Re: [sbml-interoperability] installation of libSBML 2.3.4/SBML
> Toolbox2.0.2
>
>
> Hi Sarah!
>
> Thank you very much for your very prompt reply.
>
> I gave it a try today, and now am stuck in a different place :roll: I'm
pretty
> good at this, aren't I!?
>
> Today I tried libSBML 4.2.0 (latest stable release?) and SBMLToolbox 3.1.0
(as
> you recommended)
>
> I added the MATLAB's mex to my path,
> and set the CFLAGS and LDFLAGS as described in the readme file.
>
> My first attempt gives the error
>
> Warning: You are using gcc version "4.4.4-14ubuntu5)". The version
> currently supported with MEX is "4.3.4".
> For a list of currently supported compilers see:
> http://www.mathworks.com/support/compilers/current_release/
>
> So, I went to d/l gcc 4.3.5 (I couldn't find 4.3.4), and tried it again.
>
> The gcc warning is now replaced by:
>
> mex -I/usr/local/include -I/usr/local/include -L/usr/local/lib
-L/usr/local/lib
> OutputSBML.c -lsbml
> /usr/bin/ld: cannot find -lstdc++
> collect2: ld returned 1 exit status
>
> mex: link of ' "OutputSBML.mexa64"' failed.
>
> make: *** [OutputSBML.mexglx] Error 1
>
>
> I saw in a different thread that SBMLToolbox 3.0.0 is not compatible with
> 4.0.0? Is it that I only need to change the version that I install?
>
> Thanks again!
> Celine
>
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