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?