[Debian-med-packaging] Bug#858053: Set severity grave, more speaking title

[Andreas Tille]

severity 858053 grave
retitle 858053 cutadapt does not start due to missing python-xopen dependency
thanks

I've fixed the issue in Git and added running build time tests to avoid
issues like this in future versions.  The fixed package will be uploaded
soon.

Kind regards

        Andreas.


On Mon, Mar 20, 2017 at 08:00:29PM +0600, Fedor Goncharov wrote:
> Hi Andreas,
> Yes, you are right bugreport must have grave severity.
> 
> Here is console output when I running cutudapt:
> Traceback (most recent call last):
>   File "/usr/bin/cutadapt", line 6, in <module>
>     from pkg_resources import load_entry_point
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> 3019, in <module>
>     @_call_aside
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> 3003, in _call_aside
>     f(*args, **kwargs)
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line
> 3032, in _initialize_master_working_set
>     working_set = WorkingSet._build_master()
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 655,
> in _build_master
>     ws.require(__requires__)
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 963,
> in require
>     needed = self.resolve(parse_requirements(requirements))
>   File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 849,
> in resolve
>     raise DistributionNotFound(req, requirers)
> pkg_resources.DistributionNotFound: The 'xopen>=0.1.0' distribution was not
> found and is required by cutadapt
> 
> Probably, exception rise because this file:
> /usr/lib/python3/dist-packages/cutadapt-1.12.egg-info/requires.txt in line 1
> have the string: xopen>=0.1.0
> 
> This is necessary because main script and others import xopen:
> /usr/lib/python3/dist-packages/cutadapt/scripts/cutadapt.py:72:from xopen
> import xopen
> /usr/lib/python3/dist-packages/cutadapt/filters.py:18:from xopen import
> xopen
> /usr/lib/python3/dist-packages/cutadapt/seqio.py:14:from xopen import xopen
> 
> So, xopen package not optional dependence for cutadapt.
> 
> 
> Andreas Tille писал 2017-03-20 17:04:
> >Hi again Fedor,
> >
> >I'd like to make my question to you urgent:  I have packaged
> >python-xopen and I was able to convince ftpmaster to accept it
> >quickly.  So the chance to solve this bug in Stretch with good
> >arguments to convince the release team is given.  However, your
> >"please read the docs" is not a good argument.  Please rather
> >provide a test case that proves that the current cutadapt is
> >non-functional in relevant use cases.
> >
> >Please always keep in mind that Debian maintainers like me do
> >not necessarily work with the packages we are maintaining and
> >need the help of users like you in cases like this.
> >
> >Kind regards
> >
> >       Andreas.
> >
> >On Fri, Mar 17, 2017 at 09:10:02PM +0100, Andreas Tille wrote:
> >>Hi Fedor,
> >>
> >>thanks a lot for the important hint.
> >>
> >>On Sat, Mar 18, 2017 at 12:41:12AM +0600, Fedor Goncharov wrote:
> >>> Package: python3-cutadapt
> >>> Version: 1.12-1
> >>> Severity: normal
> >>            ^^^^^^
> >>
> >>> Latest cutadapt (since 1.12) didn't work without xopen package.
> >>
> >>If you say "didn't work" this would rather be severity
> >>
> >>   grave: makes the package in question unusable or mostly so
> >>
> >>Please confirm this and I'll rise the severity to make sure
> >>this fix make it into Stretch.
> >>
> >>Kind regards
> >>
> >>     Andreas.
> >>
> >>--
> >>http://fam-tille.de
> >>
> >>_______________________________________________
> >>Debian-med-packaging mailing list
> >>Debian-med-packaging at lists.alioth.debian.org
> >>http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >>
> 
> -- 
> Fedor Goncharov
> Post graduate student,
> Institute of Molecular and Cellular Biology SB RAS
> Novosibirsk 630090
> email: fedor at mcb.nsc.ru
> web: http://www.mcb.nsc.ru
> 
> 

-- 
http://fam-tille.de