Control: reassign -1 python3-cobra 0.18.0-1 Control: retitle -1 python3-cobra: Missing dependency on python3-sbml5 Control: tags -1 patch
On Thu, Apr 23, 2020 at 03:32:06PM +0100, peter green wrote: > Source: python-cobra > Version: 0.14.2-2 > Severity: serious > > (this issue affects both 0.14.2-2 from testing and 0.18.0-1 from unstable) The problem in testing was fixed in 0.18.0-1: python-cobra (0.18.0-1) unstable; urgency=medium ... * python3-sbml is now python2-sbml5 ... -- Andreas Tille <ti...@debian.org> Mon, 20 Apr 2020 19:11:22 +0200 (I assume this meant python*3*-sbml5) > python-cobra's build-dependencies are not satisfiable in testing/unstable on > mipsel, it build-depends on python3-sbml5 and libsbml5 which are built by the > libsbml source package. libsbml has dropped support for mipsel due to linker > memory exhaustion issues. > > Since one of the dependencies is marked as <!nocheck> and since there are no > corresponding binary dependencies I presume that these are only needed for > the testsuite. >... The actual bug is that there are no corresponding binary dependencies. Warning during the build: ... dh_python3 -a -O--buildsystem=pybuild I: dh_python3 pydist:224: Cannot find package that provides python_libsbml_experimental. Please add package that provides it to Build-Depends or add "python_libsbml_experimental python3-libsbml-experimental" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info. ... This is also the root cause of the autopkgtest failure: https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-cobra/5417105/log.gz It be reproduced with: $ python3 Python 3.8.3rc1 (default, Apr 30 2020, 07:33:30) [GCC 9.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import cobra Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3/dist-packages/cobra/__init__.py", line 40, in <module> from cobra import io File "/usr/lib/python3/dist-packages/cobra/io/__init__.py", line 8, in <module> from cobra.io.sbml import read_sbml_model, write_sbml_model, \ File "/usr/lib/python3/dist-packages/cobra/io/sbml.py", line 41, in <module> import libsbml ModuleNotFoundError: No module named 'libsbml' >>> The suggested workaround works: $ cat debian/py3dist-overrides python_libsbml_experimental python3-sbml5 $ I've submitted a request for removal of the mipsel binary, let's use this bug here for the missing dependency. cu Adrian
