Arch Linux User Repository

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.

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.

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

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

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).

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

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

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

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

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