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I am trying to build libsbml and SBMLToolbox in user-space for a
Linux 2.6.32-24-generic (Ubuntu 4.4.3-4ubuntu5), Intel Xenon 64-bit machine.
I am doing the following configuration (details why at the end):
$ ./configure --prefix=$HOME --enable-m64
--with-matlab=/soft/com/packages/Matlab_2010a CC=gcc-4.2

libSBML version 4.1.0
----------------------------------------------------------------------

More information and the latest version are available online at
http://sbml.org/Software/libSBML

Please report problems using the issue tracker at
http://sbml.org/software/libsbml/issue-tracker

To contact the developers directly, email libsbml-team@caltech.edu

Configured on host "crush"
host type = linux
host vendor = unknown
host operating system = linux-gnu
host CPU architecture = x86_64

General build flags:
CC = gcc-4.2
CXX = g++
CPPFLAGS = -DLINUX -I/homes/devoid/include
CFLAGS = -m64
CFLAGS_ARCH =
CXXFLAGS = -m64
CXXFLAGS_ARCH =
LDFLAGS = -L/homes/devoid/lib -m64
LDFLAGS_ARCH =
LIBS = -lm -lz -lbz2

XML parser library configuration:
XML library = libxml2
CPPFLAGS for XML = -I/usr/include/libxml2
LDFLAGS for XML =
LIBS for XML = -lxml2

Other libSBML configuration settings:
Installation $prefix = /homes/devoid
Using MATLAB with path = /soft/com/packages/Matlab_2010a/bin/matlab
Using zlib with path = autodetect
Using bzip2 with path = autodetect

Other potentially important settings:
Compression support is enabled for .zip, .gz and .bz2 files
Value of $LD_LIBRARY_PATH =
MATLAB architecture assumed =
MATLAB binary file extension =
----------------------------------------------------------------------

With make, I get the following errors:
make[3]: Entering directory
`/nfs/mcs-homes140/devoid/libsbml-4.1.0/src/bindings/matlab'
env MATLABROOT= ARCH= Arch= \
CFLAGS="-m64" /homes/devoid/libsbml-4.1.0/doltlibtool --tag=CC
--mode=link /soft/com/packages/Matlab_2010a/bin/mex \
ARCH= Arch= -f mexopts-R2009-R2010.sh \
-o TranslateSBML. TranslateSBML.c -I../.. -I../../../include
-L../.. ../../libsbml.la
mkdir .libs
/soft/com/packages/Matlab_2010a/bin/mex ARCH= Arch= -f
mexopts-R2009-R2010.sh -o .libs/TranslateSBML. TranslateSBML.c -I../..
-I../../../include -L/nfs/mcs-homes140/devoid/libsbml-4.1.0/src
../../.libs/libsbml.so -L/homes/devoid/lib /usr/lib/libxml2.so -lz -lbz2
-Wl,--rpath -Wl,/homes/devoid/lib
In file included from ../../../include/sbml/annotation/RDFAnnotation.h:61,
from ../../sbml/SBase.h:126,
from ../../sbml/SBMLDocument.h:239,
from ../../sbml/SBMLTypes.h:30,
from TranslateSBML.c:35:
../../../include/sbml/annotation/ModelHistory.h:888:7: warning: missing
terminating ' character
creating TranslateSBML.
cp -f .libs/TranslateSBML. .
cp: cannot stat `.libs/TranslateSBML.': No such file or directory
make[3]: *** [TranslateSBML.] Error 1
make[3]: Leaving directory
`/nfs/mcs-homes140/devoid/libsbml-4.1.0/src/bindings/matlab'
make[2]: *** [matlab-recurse] Error 2
make[2]: Leaving directory
`/nfs/mcs-homes140/devoid/libsbml-4.1.0/src/bindings'
make[1]: *** [bindings-recurse] Error 2
make[1]: Leaving directory `/nfs/mcs-homes140/devoid/libsbml-4.1.0/src'
make: *** [src-recurse] Error 2

The lack of an extension on TranslateSBML. seems to suggest something wrong
with the configuration of 64 bit versus 32 bit extension names.
If I look in libsbml-4.1.0/src/bindings/matlab/.lib/ I see
TranslateSBML..mexa64 , the two dots also being cause for concern. I've also
tried renaming this file to the "TranslateSBML."
as the makefile seems to expect: make runs without errors, make install runs
fine, but of course, TranslateSBML doesn't seem to exist when I run the
tests after building and installing SBMLToolbox. At this point I'm at a
loss... I think I want to get "TranslateSBML.mexa64" then have the makefile
put that in the proper place, but I can't seem to do that.


So some details on each of the configure flags: --prefix=$HOME so I install
in user space.
--enable-m64 for 64 bit. The machine I'm on has both 64-bit and 32-bit
matlab packages and I've tried this, --enable-m32 and the "default" all
producing the same error
$ file `which mex` returns /usr/bin/mex: symbolic link to `pdftex' so I do
--with-matlab=/soft/com/packages/Matlab_2010a to direct it to the MATLAB mex
utility.
Finally, CC=gcc-4.2 because mex complains with anything more recent:
/soft/com/packages/Matlab_2010a/bin/mex ARCH= Arch= -f
mexopts-R2009-R2010.sh -o .libs/TranslateSBML. TranslateSBML.c -I../..
-I../../../include -L/nfs/mcs-homes140/devoid/libsbml-4.1.0/src
../../.libs/libsbml.so -L/homes/devoid/lib /usr/lib/libxml2.so -lz -lbz2
-Wl,--rpath -Wl,/homes/devoid/lib

Warning: You are using gcc version "4.4.3-4ubuntu5)". The version
currently supported with MEX is "4.2.3".
For a list of currently supported compilers see:
http://www.mathworks.com/support/compilers/current_release/

However, CC isn't getting passed to mex with either this or export
CC=gcc-4.2 so I ended up doing $ export PATH=~/bin:$PATH and $ ln -s `which
gcc-4.2` ~/bin/gcc which finally stops that mex complaint. Removing the
configure flag then produces the same result, and the same TranslateSBML
errors, as including it.

Sorry for the long email and thank you in advance for your help!
~ Scott Devoid
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