[Debian-med-packaging] Bug#858053: python3-cutadapt: Please read the official cutadapt changelog and add `xopen` in the package dependences. Thank you!

[Fedor Goncharov]

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