Package Details: libsbml 5.20.4-1

Git Clone URL: https://aur.archlinux.org/libsbml.git (read-only, click to copy)
Package Base: libsbml
Description: XML-based description language for computational models in systems biology
Upstream URL: https://github.com/sbmlteam/libsbml
Licenses: LGPL
Submitter: mschu
Maintainer: mschu
Last Packager: mschu
Votes: 5
Popularity: 0.000000
First Submitted: 2011-04-24 08:52 (UTC)
Last Updated: 2024-09-09 09:33 (UTC)

Dependencies (12)

Sources (1)

Latest Comments

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pekkarr commented on 2024-04-21 15:19 (UTC)

This fails to build in a clean chroot.

/build/libsbml/src/libsbml-5.20.2/src/sbml/xml/LibXMLParser.cpp: In member function ‘virtual bool LibXMLParser::parseNext()’:
/build/libsbml/src/libsbml-5.20.2/src/sbml/xml/LibXMLParser.cpp:427:46: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlErrorPtr’ {aka ‘_xmlError*’} [-fpermissive]
  427 |     xmlErrorPtr libxmlError = xmlGetLastError();
      |                               ~~~~~~~~~~~~~~~^~
      |                                              |
      |                                              const xmlError* {aka const _xmlError*}

pbordron commented on 2022-05-28 21:59 (UTC)

Got an error when installing the version 5.19..5

error: failed to commit transaction (conflicting files)
libsbml: /usr/share/cmake/Modules/FindZLIB.cmake exists in filesystem (owned by cmake)
Errors occurred, no packages were upgraded.
 -> exit status 1

I think it is related with this issue -> https://github.com/sbmlteam/libsbml/issues/219

I did a quick in the package part by removing problematic files.

package() {
  cd "$srcdir"/build-$pkgver
  DESTDIR="$pkgdir" cmake -DCMAKE_INSTALL_PREFIX=/usr -P cmake_install.cmake
  rm "$pkgdir"/usr/share/cmake/Modules/FindZLIB.cmake
  rm "$pkgdir"/usr/share/cmake/Modules/FindBZ2.cmake
}

please, could you update the build part using -DWITH_STABLE_PACKAGES=ON option instead of the individual -DENABLE_ options?


build() {
  cd "$srcdir"/$pkgname-$pkgver
  ./autogen.sh

  mkdir -p "$srcdir"/build-$pkgver && cd "$srcdir"/build-$pkgver
  cmake ../$pkgname-$pkgver \
    -DCMAKE_INSTALL_PREFIX:PATH=/usr \
    -DCMAKE_INSTALL_LIBDIR:PATH=lib \
    -DWITH_LIBXML=ON \
    -DWITH_EXPAT=OFF \
    -DWITH_BZIP2=ON \
    -DWITH_ZLIB=ON \
    -DWITH_PYTHON=ON \
    -DWITH_STABLE_PACKAGES=ON

  make
}

pbordron commented on 2022-01-12 14:57 (UTC) (edited on 2022-01-12 14:58 (UTC) by pbordron)

Thanx for the update.

I think it is possible to simplify the recipe by replacing all the -DENABLE_*=ON in build section by -DWITH_STABLE_PACKAGES=ON. This way, new stable packages will be automatically build with next versions of libsbml.

It is also possible to activate experimental packages by using -DWITH_ALL_PACKAGES=ON instead. Maybe it will be interesting to have a libsbml-experimental like SBMLTeam provides for conda

pbordron commented on 2022-01-12 12:36 (UTC) (edited on 2022-01-12 12:36 (UTC) by pbordron)

I just saw that a pre-release version (5.19.2) corrects the bug

https://github.com/sbmlteam/libsbml/releases/tag/v5.19.2

pbordron commented on 2022-01-12 11:03 (UTC)

Got this error with python-3.10

https://github.com/sbmlteam/libsbml/issues/173

Can be corrected with this patch:

https://github.com/sbmlteam/libsbml/commit/7843361b3fb6d13658928105e4635a01478ba70e

mschu commented on 2017-06-06 23:24 (UTC)

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 (UTC)

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 (UTC)

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

vdubikhin commented on 2017-05-27 23:41 (UTC) (edited on 2017-05-28 01:42 (UTC) by vdubikhin)

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 (UTC)

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).

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