Re: installation of libSBML 2.3.4/SBML Toolbox2.0.2
26 Jan '11 14:10
-----BEGIN PGP SIGNED MESSAGE-----
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
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
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.
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
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:
> 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!
University of Applied Science Koblenz
Department of Mathematics and Techniques
Gene Expression Analysis Laboratory
Biomolecular Modelling Laboratory
Cancer Research UK
London Research Institute
44, Lincoln's Inn Fields
London, WC2A 3LY
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.15 (GNU/Linux)
Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org/
-----END PGP SIGNATURE-----
Powered by FUDforum. (Copyright Advanced Internet Designs Inc.)