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Hi Celine

I'm sorry you are having a problem. The difficulty is that indeed
libsbml.2.3.4 and SBMLToolbox-2.0.0 have been superseded with more
recent versions.

I'm not sure what functionality of SBMLToolbox SBML_SAT uses but it is
likely that it should work with the latest versions; I tried very hard
to be backward compatible as it is something that really annoys me with
other software :-)

For the record your issue with the libsbml-2.3.4 build is that it was
written before Xerces-3 existed and thus does not link against the now
more recent version of Xerces. If you were to try

./configure --with-expat --with-matlab=/Applications/Programming/MATLAB2010b

it may work. I cannot say it will definitely work as different versions
of MATLAB can prove problematic and libsbml-2.3.4 predates MATLAB2010 by
a number of years.

I would try using SBML-SAT with the later versions of libsbml and
SBMLToolbox (try SBMLToolbox-3.1.2). It may just work.

Let me know how it goes.

Sarah


celine wrote:
> I am trying to install SBML-SAT on a Ubuntu 10.10 64bit system.
>
> I have tried several different combinations of libsbml and SBML Toolbox with varying degrees of... failure :cry: (if those failures are of any interest, I can list them)
>
> I've been advised to use libsbml 2.3.4 and SBML Toolbox 2.0.2, as SBML-SAT has not yet been updated for the latest libsbml/SBML Toolbox.
>
> On my latest attempt:
> ./configure --with-matlab=Application/Programming/MATLABR2010b
>
> succeeds, and spits out:
> Build Settings for libsbml v2.3.4:
> ----------------------------------
> host type = linux
> install dir = /usr/local
> XML library = Xerces-C++
> CC = gcc
> CXX = g++
> CFLAGS = -g -O2
> CXXFLAGS = -g -O2
> CPPFLAGS = -DLINUX
> LDFLAGS =
> LIBS = -lm
> enable memory tracing? = no
> use libcheck? = no
> use SWIG? = no
> use Python? = no
> use Perl? = no
> use Java? = no
> use Matlab? = Application/Programming/MATLABR2010b
> use Lisp = no
>
> (Which I think it is successful?) Then, 'build' seems to be unsuccessful with the following errors:
>
> make[2]: Entering directory `/home/celine/Downloads/libsbml-2.3.4/src/math'
> g++ -I.. -I. -DLINUX -g -O2 -fPIC -MT MathMLHandler.o -MD -MP -MF ".deps/MathMLHandler.Po" -c -o MathMLHandler.o MathMLHandler.cpp
> MathMLHandler.cpp: In member function �void MathMLHandler::characters(const XMLCh*, unsigned int)�:
> MathMLHandler.cpp:381: error: �isAllWhiteSpace� is not a member of �xercesc_3_1::XMLString�
> make[2]: *** [MathMLHandler.o] Error 1
> make[2]: Leaving directory `/home/celine/Downloads/libsbml-2.3.4/src/math'
> make[1]: *** [math-recurse] Error 2
> make[1]: Leaving directory `/home/celine/Downloads/libsbml-2.3.4/src'
> make: *** [src-recurse] Error 2
>
>
> First off, is it necessary to use libSBML 2.3.4? Initially I had installed (successfully) libSBML 4.2.0 before I read the dependencies statements of SBMLToolbox 3.0 and SBML-SAT. However, I can imagine that SBML toolbox 3.0 would not necessarily update the dependencies list, especially since there are newer editions already available.
>
> If it is necessary to use libSBML 2.3.4, how can I fix the above errors?
>
> Thanks for your help!
> Celine
> ____________________________________________________________
> To manage your sbml-interoperability list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
>
> For a web interface to the sbml-interoperability mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the sbml-interoperability list,
> contact sbml-team@caltech.edu
>

____________________________________________________________
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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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Dear Frank,

I think I got the same result... I will write out the steps I took in case I did something wrong.

1. change the file '/libsbml-4.2.0/src/bindings/matlab/make.ini'
2. in terminal:
cd /home/celine/Downloads/libsbml-4.2.0
./configure --with-matlab=Application/Programming/MATLAB\ R2010b
make
sudo make install
sudo ldconfig
(Note: this time, there were many more lines coming out after the 'make install' command, but in the end looks similar to previous attempts)

3. in new terminal:
PATH="/usr/local/MATLAB/R2010b/bin:$PATH"
echo $PATH
/usr/local/MATLAB/R2010b/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
which mex
/usr/local/MATLAB/R2010b/bin/mex
cd /home/celine/Downloads/SBMLToolbox-3.0.0/toolbox
export CFLAGS=-I/usr/local/include
export LDLAGS=-L/usr/local/lib
make

(Many many warnings follow, then finally
mex: compile of ' "OutputSBML.c"' failed.

make: *** [OutputSBML.mexglx] Error 1 )

Dear Torbjoern,

I was unable to find g++ 4.1 (although I had gcc 4.1 and cpp 4.1).

Just to make sure, did I do the symbolic links properly?:

sudo rm /usr/bin/gcc
sudo ln -s /usr/bin/gcc-4.1 /usr/bin/gcc

sudo rm /usr/bin/cpp
sudo ln -s /usr/bin/cpp-4.1 /usr/bin/cpp

Nonetheless, I tried it with just changing the above two symbolic links. I guess it's probably no surprise, but I got the same result as before

What is the best way to get g++ 4.1? In the past, I just use the "Ubuntu Software Center". If that fails, I go to "http://packages.ubuntu.com". This time, it wouldn't let me install gcc-4.1-base (because I had a newer version installed). It wouldn't let me remove the newer version, because it's an "essential part" of my system.

Actually these questions should belong in a Ubuntu forum... Sorry!

Thanks everyone so far for all the help: Sarah, Frank, Torbjoern

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Hi Celine,

the symlinks should be ok. There should be the g++ as well in both
versions. I haven't got access to a Ubuntu machine right now, only my
openSUSE one, so I cannot check how that works on Ubuntu, sorry.

For the differences and relations of gcc, cpp and g++ this might be helpful:
http://stackoverflow.com/questions/172587/what-is-the-difference-between-g-and-gcc

Good luck with this. However, it might be better using Frank's suggested
solution.

Cheers,
Torbjoern


On 28/01/11 00:21, celine wrote:
>
> Dear Torbjoern,
>
> I was unable to find g++ 4.1 (although I had gcc 4.1 and cpp 4.1).
>
> Just to make sure, did I do the symbolic links properly?:
>
> sudo rm /usr/bin/gcc
> sudo ln -s /usr/bin/gcc-4.1 /usr/bin/gcc
>
> sudo rm /usr/bin/cpp
> sudo ln -s /usr/bin/cpp-4.1 /usr/bin/cpp
>
> Nonetheless, I tried it with just changing the above two symbolic links. I guess it's probably no surprise, but I got the same result as before :lol:
>
> What is the best way to get g++ 4.1? In the past, I just use the "Ubuntu Software Center". If that fails, I go to "http://packages.ubuntu.com". This time, it wouldn't let me install gcc-4.1-base (because I had a newer version installed). It wouldn't let me remove the newer version, because it's an "essential part" of my system.
>
> Actually these questions should belong in a Ubuntu forum... Sorry!
>
> Thanks everyone so far for all the help: Sarah, Frank, Torbjoern :D
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Hello Celine

>
> So far, so good, right?
>

Congratulations ... at this point you completed installing the Matlab
bindings (or translate SBML) ... if you were to start Matlab in this folder
you could run TranslateSBML('test.xml') and you would get the translated
structure. So this is great for part 1). You might want to make sure the
generated .mexa64 file is in the Matlab path from now on!.

>
> ===Now, for the SBMLToolbox
>
> $ PATH="/usr/local/MATLAB/R2010b/bin:$PATH"
> $ echo $PATH
> > /usr/local/MATLAB/R2010b/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:
> > /usr/bin:/sbin:/bin:/usr/games
>
> $ which mex
> > /usr/local/MATLAB/R2010b/bin/mex
>
>
> $ cd /home/celine/Downloads/SBMLToolbox-3.0.0/toolbox
> $ export CFLAGS=-I/usr/local/include
> $ export LDLAGS=-L/usr/local/lib
>
> ===First try:
>
> $ make
> > 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/
>
>
> (nothing happens? no warnings, no errors, nothing. only the above)
>

Stop! ... at this point ... if you closely look at the directory you will
find that you have a shiny new 'OutputSBML.mexa64' in the directory. And
again you are done :) If you add this directory to your Matlab path
(together with the one from above), you can now run:

model = TranslateSBML('test.xml')
OutputSBML(model)

And you would find a dialog popping up asking you for the filename where to
safe the file too.

Sorry if this is not as intuitive as it could be ... in the next release we
will be providing scripts with better output. Please let me know if you
continue to have trouble

Best
Frank



____________________________________________________________
To manage your sbml-interoperability list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability

For a web interface to the sbml-interoperability mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-interoperability list,
contact sbml-team@caltech.edu