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.
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Fedor Goncharov
Post graduate student,
Institute of Molecular and Cellular Biology SB RAS
Novosibirsk 630090
email: fe...@mcb.nsc.ru
web: http://www.mcb.nsc.ru
