[Debian-med-packaging] Bug#958538: python-cobra build-dependencies unsatisfiable on mipsel

Adrian Bunk bunk at debian.org
Sun May 10 19:28:10 BST 2020


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 <tille at 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



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