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Posts: 11
Registered:
January 2011
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Re: installation of libSBML 2.3.4/SBML Toolbox2.0.2
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28 Jan '11 08:42
 
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Hi Frank,
Thanks again for all your help so far. Here are my latest steps (and results):
first, I changed (yesterday) the file '/libsbml-4.2.0/src/bindings/matlab/Makefile.in
(sorry for lack of brain yesterday)
$ cd /home/celine/Downloads/libsbml-4.2.0
$ ./configure --with-matlab=/usr/local/MATLAB/R2010b
(note: I realize what I understood wrong from the "how to install guide" -- From the example given I concluded there is some special shortcut to typing the path by using the "Applications" menu in the Ubuntu GUI... opps!)
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Other libSBML configuration settings:
Installation $prefix = /usr/local
Using MATLAB with path = /usr/local/MATLAB/R2010b/bin/matlab
Other potentially important settings:
Value of $LD_LIBRARY_PATH =
MATLAB architecture assumed = glnxa64
MATLAB binary file extension = mexa64
Warning: reading/writing compressed SBML in this copy of libSBML
is not supported or has not been enabled. If this was not your
intention, please check the --with-zlib, -with-bzip2, and/or
--enable-compression options.
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$ cd src/bindings/matlab
$ make
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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/
In file included from ../../../include/sbml/annotation/RDFAnnotation.h:61,
from ../../sbml/SBase.h:126,
from ../../sbml/SBMLDocument.h:265,
from ../../sbml/SBMLTypes.h:30,
from TranslateSBML.c:35:
../../../include/sbml/annotation/ModelHistory.h:888: warning: missing terminating ' character
creating TranslateSBML.mexa64
cp -f .libs/TranslateSBML.mexa64
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So far, so good, right?
Now I wasn't sure whether or not I need to "make" in the original directory, but I had an inkling that I probably would need to, so I did.
$ cd ..
$ cd ..
$ cd ..
$ pwd
/home/celine/Downloads/libsbml-4.2.0
$ make
(a lot of text, some missing from buffer)
$ sudo make install
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Makefile:444:
The installation of libSBML is finished. On certain platforms
(such as Linux), you will also need to do one of the following:
1) run 'ldconfig' (see the man page if this is unfamiliar)
2) set the LD_LIBRARY_PATH (or equivalent) environment variable
to contain the path "/usr/local/lib" so that programs can
find the libSBML library at run-time.
/home/celine/Downloads/libsbml-4.2.0/config/install-sh -c libsbml.pc -m 0644 "/usr/local/lib/pkgconfig/libsbml.pc"
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$ sudo ldconfig
(nothing comes out, is this expected?)
===Now, for the SBMLToolbox
$ PATH="/usr/local/MATLAB/R2010b/bin:$PATH"
$ echo $PATH
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/usr/local/MATLAB/R2010b/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
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$ which mex
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/usr/local/MATLAB/R2010b/bin/mex
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$ cd /home/celine/Downloads/SBMLToolbox-3.0.0/toolbox
$ export CFLAGS=-I/usr/local/include
$ export LDLAGS=-L/usr/local/lib
===First try:
$ make
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mex -I/usr/local/include -I/usr/local/include -L/usr/local/lib OutputSBML.c -lsbml
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/
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(nothing happens? no warnings, no errors, nothing. only the above)
===2nd try: try sudo?
$ sudo make
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[sudo] password for celine:
mex -I/usr/local/include -L/usr/local/lib OutputSBML.c -lsbml
make: mex: Command not found
make: *** [OutputSBML.mexglx] Error 127
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(again, no warnings, no errors...)
===3rd try: change to gcc 4.3, just in case
$ sudo rm /usr/bin/gcc
$ sudo ln -s /usr/bin/gcc-4.3 /usr/bin/gcc
$ cd /home/celine/Downloads/SBMLToolbox_3.1.2/toolbox
$ export CFLAGS=-I/usr/local/include
$ export LDLAGS=-L/usr/local/lib
$ make
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mex -I/usr/local/include -I/usr/local/include -L/usr/local/lib OutputSBML.c -lsbml
make: mex: Command not found
make: *** [OutputSBML.mexglx] Error 127
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$ sudo make
mex -I/usr/local/include -L/usr/local/lib OutputSBML.c -lsbml
make: mex: Command not found
make: *** [OutputSBML.mexglx] Error 127
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Lastly, I'm not sure if this is helpful: I googled the error, and found this post: http://ubuntuforums.org/showthread.php?t=910171
my "$ which mex" gives
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/usr/local/MATLAB/R2010b/bin/mex
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 any more tips?
Sorry for the very long post, and thanks again for your help! If you ever need someone to make something not work, I'm happy to help! 
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