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Ok, this error means that after compiling the bindings they failed to start on your system. Please change into the directory src/bindings/matlab (from within matlab) and try the bindings and report all messages that you get when you type

TranslateSBML('test.xml')

if the error mentions something like an incompatibility with the standard c++ library, you might want to set the LD_PRELOAD environment variable to its location to be sure that one is loaded first.

http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-issues.html#matlab-linux

best
Frank

On May 7, 2012, at 4:35 PM, ayesha wrote:

>
> Hi Frank
>
> Thanks for the tip. I ran buildSBML.m from inside MATLAB and this is output I get
>
> * Doing preliminary checks of runtime environment ...
> - This appears to be MATLAB and not Octave.
> - MATLAB reports the OS is 64-bit Linux.
>
> Constructing the libSBML MATLAB interface.
>
> * Trying to establish our location ...
> - We are in the libSBML subdirectory for Matlab.
> - We appear to be in the libSBML source tree.
> - We have write access here! That makes us happy.
> * Locating libSBML library and include files ...
> - Found /home/ayesha/Downloads/SOFTWARE/libsbml-5.4.1/src/.libs/libsbml.so
> - Root of includes is /home/ayesha/Downloads/SOFTWARE/libsbml-5.4.1/src
> * Creating mex files in /home/ayesha/Downloads/SOFTWARE/libsbml-5.4.1/src/bindings/matlab
> - Building TranslateSBML ...
>
> Warning: You are using gcc version "4.6.1-9ubuntu3)". 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/
>
> - Building OutputSBML ...
>
> Warning: You are using gcc version "4.6.1-9ubuntu3)". 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/
>
> OutputSBML.c: In function ‘mexFunction’:
> OutputSBML.c:193:14: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
>
> Successfully finished. If appropriate, please run "installSBML" next.
>
>
>
> Next, I ran installSBML.m, and this is what I get
>
>
> Installing the libSBML MATLAB interface.
>
> * Doing preliminary checks of runtime environment ...
> - This appears to be MATLAB and not Octave.
> - MATLAB reports the OS is 64-bit Linux.
> Checking for executables ...
> Executables found
> * Trying to establish our location ...
> - We are in the libSBML subdirectory for Matlab.
> - We appear to be in the libSBML source tree.
> - We have write access here! That makes us happy.
> Checking for libraries ...
> adding /home/ayesha/Downloads/SOFTWARE/libsbml-5.4.1/src/bindings/matlab to the path
>
> Testing the installation.
>
> checking for TranslateSBML
> Installation failed - MATLAB cannot find all the libraries
> Add the path to the libraries to your path
> If this fails please contact the libsbml-team@caltech.edu
>
>
>
> These are files which are present in the /src/bindings/matlab folder
>
> AUTHORS.txt Contents.m isoctave.m matlab-tags-regexp.txt mexopts-R2009-R2010.sh README.txt TranslateSBML.m
> buildSBML.m ConvertFormulaToMathML.m isSBML_Model.m mexopts-lion.sh OutputSBML.c test TranslateSBML.mexa64
> CheckAndConvert.m FindMatlab.cmake Makefile mexopts-R2007.sh OutputSBML.m test.xml
> CMakeLists.txt installSBML.m Makefile.in mexopts-R2008.sh OutputSBML.mexa64 TranslateSBML.c
>
>
> Just to be sure that I understand this right, when I do
> echo $LD_LIBRARY_PATH
>
> I do see, :/usr/local/lib
>
> and when I navigate to the above dir, I see
>
>
> -rwxr-xr-x 1 root root 5535924 2012-05-07 09:14 libsbml.so.5.4.1
> lrwxrwxrwx 1 root root 16 2012-05-07 09:14 libsbml.so.5 -> libsbml.so.5.4.1
> lrwxrwxrwx 1 root root 16 2012-05-07 09:14 libsbml.so -> libsbml.so.5.4.1
> -rwxr-xr-x 1 root root 840 2012-05-07 09:14 libsbml.la
> -rw-r--r-- 1 root root 16252668 2012-05-07 09:14 libsbml.a
> -rwxr-xr-x 1 root root 6594823 2012-05-07 09:14 libsbmlj.so
>
>
> Any suggestion here would be helpful.
>
> Thanks!
> ~Ayesha
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