Package Details: libsbml 5.15.0-1

Git Clone URL: https://aur.archlinux.org/libsbml.git (read-only)
Package Base: libsbml
Description: XML-based description language for computational models in systems biology
Upstream URL: http://sbml.org/Software/libSBML
Licenses: LGPL
Submitter: mschu
Maintainer: mschu
Last Packager: mschu
Votes: 5
Popularity: 0.000457
First Submitted: 2011-04-24 08:52
Last Updated: 2017-06-03 17:09

Latest Comments

mschu commented on 2017-06-06 23:24

I tracked this down to the "groups" package. If you don't need it see if disabling helps, I will see if I find the exact error.

deeenes commented on 2017-06-06 08:45

The compiled Python2 module throws this error on import:

>>> import libsbml
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "/usr/lib/python2.7/site-packages/libsbml/__init__.py", line 18, in <module>
_libsbml = swig_import_helper()
File "/usr/lib/python2.7/site-packages/libsbml/__init__.py", line 17, in swig_import_helper
return importlib.import_module('_libsbml')
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
ImportError: /usr/lib/python2.7/site-packages/libsbml/_libsbml.so: undefined symbol: _ZN5Group9unsetKindEv

I am aware that webpage of libSBML says: "If a user's environment includes an old version of this library file, and it is picked up at run-time instead of the correct library version, linking may fail with mysterious errors about undefined symbols."

However either at compile time or run time I have only version 5.15.0 of libsbml:

$ ldd /usr/lib/python2.7/site-packages/libsbml/_libsbml.so
linux-vdso.so.1 (0x00007fff40784000)
libsbml.so.5 => /usr/lib/libsbml.so.5 (0x00007fcff40e4000)
libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00007fcff3cfa000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fcff3adc000)
libutil.so.1 => /usr/lib/libutil.so.1 (0x00007fcff38d9000)
libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007fcff3571000)
liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007fcff334b000)
libicui18n.so.59 => /usr/lib/libicui18n.so.59 (0x00007fcff2ecb000)
libicuuc.so.59 => /usr/lib/libicuuc.so.59 (0x00007fcff2b1a000)
libicudata.so.59 => /usr/lib/libicudata.so.59 (0x00007fcff1007000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fcff0e03000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007fcff0bec000)
libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007fcff09dc000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007fcff0651000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007fcff033f000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007fcfeff9a000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fcfefd83000)
/usr/lib64/ld-linux-x86-64.so.2 (0x000055d1c974b000)

$ ls -la /usr/lib/libsbml.so.5
lrwxrwxrwx 1 root root 17 Jun 4 17:53 /usr/lib/libsbml.so.5 -> libsbml.so.5.15.0

$ pacman -Qs libsbml
local/libsbml 5.15.0-1
XML-based description language for computational models in systems biology

I also checked if I have any other libsbml in any other path used by gcc or ld, but found nothing else.

mschu commented on 2017-06-03 17:09

Fixed, thank you. Also enabled Ruby support by default, but not Java.

vdubikhin commented on 2017-05-27 23:41

I have noticed that, although your package downloads core+packages version of the library, additional packages are not installed by default. If possible, could you, please, modify your package file to include those extra packages? To do so you need to change configure command to look like this:

./configure --prefix=/usr \
--with-python=yes --with-python-interpreter=/usr/bin/python2 \
--with-java=no \
--with-perl=yes \
--with-octave=no \
--with-csharp=no \
--with-ruby=no \
--with-matlab=no \
--enable-layout=yes \
--enable-comp=yes \
--enable-fbc=yes \
--enable-qual=yes --enable-groups=yes

jakobcreutzfeldt commented on 2014-06-13 09:40

The build fails for me (including on the latest version, 5.10.0) unless I override the Make parrallel-build argument (I have to add "-j1" to the "make" command in the build function).

mschu commented on 2013-03-20 17:02

I will update this once I get home (one week from now). If that's too late, please someone paste a PKGBUILD.

mschu commented on 2013-03-11 20:36

You are right, that must have gotten lost with the last update. Fixed.

Herk commented on 2013-03-11 20:31

Should not swig be a dependency? Without it I was not able to install the package.

mschu commented on 2013-02-04 10:05

Oops, uploaded the wrong PKGBUILD by mistake. Fixed now.

menta commented on 2013-02-04 10:02

The first line of the 'package' function should be changed to 'cd "$srcdir/$_pkgname-$pkgver-Source"'.

mschu commented on 2012-08-05 14:35

Updated to 5.6.0 and removed the CMake dependency. The reason it was used in the first place was that the flags for the bindings in configure were not working - they are now, so we can use it directly.

The issues with swig are said to be build issues in the link you provided. Building worked fine with the latest swig, so I'm keeping that.

I don't see an easy way to python 2 and 3 at the same time, so I'll leave it to build with python2 because most of the other simulation software has not moved to version 3 yet.

In general, you will not want to just use ./configure, make, and make install but to modify the PKGBUILD to your needs, because otherwise pacman can not track the files on your harddrive and the dependency tree.

essenceoffoo commented on 2012-08-04 08:40

Does it really make sense to use CMake directly? In the README.txt it says you can just use the old fashioned ./configure && make && make install. You can supply useful options at the configuration step that are much cleaner than the CMake-options (at least in my opinion).

I just installed it that way with ./configure options that are specific to my plans (but I didn't create a package).

The newest release (5.6.0) also works with Python3 (both building and binding)

Compatibility note: It may make sense to use an older version of swig (version 2.0.4 see http://sbml.org/Forums/index.php?t=tree&goto=7657&rid=2 ) for creating scripting language bindings.