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Hi Celine,

I had the same issues while preparing my setup here and on a different
machine as well. The problem at that time was binding the libSBML 4.0.1
to the 2010-Matlab together with a recent gcc 4.4.x.

I solved the problem by installing the gcc 4.1 (found in the
repositories; 4.2 should work as well) in parallel and just changed the
symlinks (make sure, you change them not only for gcc, but also for g++
and cpp) in /usr/bin to the version I want to use. With 4.1 everything
compiled well.
I did that on a Ubuntu 9.04 and on a openSUSE 11.3 machine, both with
Matlab 2010a and libSBML 4.0.1 and SBMLToolbox 3.1.2 and everything in
64bit.

Hope, that might help you a little bit. Installing libSBML and
SBMLToolbox with respect to MATLAB has somehow and unfortunately always
been a little pain.

Cheers,
Torbjoern


PS: To make it a little more clear with the symlinks (`ln -s <source>
<dest>`), I'll give the structure of /usr/bin/gcc*, /usr/bin/g++* and
/usr/bin/cpp*

myself@tk-laptop-linux64:/usr/bin> ls -l gcc*
lrwxrwxrwx 1 root root 7 2010-09-10 10:38 gcc -> gcc-4.5
- -rwxr-xr-x 1 root root 135848 2010-07-05 13:20 gcc-4.1
- -rwxr-xr-x 1 root root 267912 2010-07-01 19:29 gcc-4.5
myself@tk-laptop-linux64:/usr/bin> ls -l g++*
lrwxrwxrwx 1 root root 7 2010-09-10 10:38 g++ -> g++-4.5
- -rwxr-xr-x 1 root root 139944 2010-07-05 13:20 g++-4.1
- -rwxr-xr-x 1 root root 272008 2010-07-01 19:29 g++-4.5
myself@tk-laptop-linux64:/usr/bin> ls -l cpp*
lrwxrwxrwx 1 root root 7 2010-09-10 10:38 cpp -> cpp-4.5
- -rwxr-xr-x 1 root root 135848 2010-07-05 13:20 cpp-4.1
- -rwxr-xr-x 1 root root 272008 2010-07-01 19:29 cpp-4.5

As you see, after compiling everything, I switched back to the v4.5.



On 26/01/11 21:22, celine wrote:
>
> 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
>

- --
Torbjoern Klatt
eMail: torbjoern@torbjoern-klatt.de
www: http://www.torbjoern-klatt.de/

University of Applied Science Koblenz
RheinAhrCampus Remagen
Department of Mathematics and Techniques
Suedallee 2
53424 Remagen
Germany
email: tklatt@rheinahrcampus.de

Gene Expression Analysis Laboratory
and
Biomolecular Modelling Laboratory
Cancer Research UK
London Research Institute
44, Lincoln's Inn Fields
London, WC2A 3LY
United Kingdom
email: torbjoern.klatt@cancer.org.uk
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