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Groups > linux.debian.bugs.rc > #279747

Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

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Source: gffread
Version: 0.11.8-1
Severity: serious
X-Debbugs-CC: debian-ci@lists.debian.org, gff2aplot@packages.debian.org
Tags: sid bullseye
User: debian-ci@lists.debian.org
Usertags: needs-update
Control: affects -1 src:gff2aplot

Dear maintainer(s),

With a recent upload of gff2aplot the autopkgtest of gffread fails in
testing when that autopkgtest is run with the binary packages of
gff2aplot from unstable. It passes when run with only packages from
testing. In tabular form:

                       pass            fail
gff2aplot              from testing    2.0-12
gffread                from testing    0.11.8-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of gff2aplot to
testing [1]. Of course, gff2aplot shouldn't just break your autopkgtest
(or even worse, your package), but it seems to me that the change in
gff2aplot was intended and your package needs to update to the new
situation. If you can't fix the issue which triggers the warning, you
can add the allow-stderr restriction for your test.

If this is a real problem in your package (and not only in your
autopkgtest), the right binary package(s) from gff2aplot should really
add a versioned Breaks on the unfixed version of (one of your)
package(s). Note: the Breaks is nice even if the issue is only in the
autopkgtest as it helps the migration software to figure out the right
versions to combine in the tests.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=gff2aplot

https://ci.debian.net/data/autopkgtest/testing/amd64/g/gffread/5834059/log.gz

autopkgtest [01:19:28]: test run-tests:  - - - - - - - - - - stderr - -
- - - - - - - -
Warning: invalid start coordinate at line:
#name1:name2		source		feature		beg1:beg2	end1:end2	score	strand	frame
group	comment
Warning: invalid start coordinate at line:
#name1:name2		source		feature		beg1:beg2	end1:end2	score	strand	frame
group	comment
autopkgtest [01:19:28]: @@@@@@@@@@@@@@@@@@@@ summary
run-tests            FAIL stderr: Warning: invalid start coordinate at line:

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Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Paul Gevers <elbrus@debian.org> - 2020-06-09 21:40 +0200
  Processed: gffread: autopkgtest needs update for new version of  gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-06-09 21:40 +0200
  Bug#962553: Bugfix: Patched gff2aplot Pranav Ballaney <ballaneypranav@gmail.com> - 2020-06-15 17:00 +0200
  Bug#962553: marked as done (gffread: autopkgtest needs update for  new version of gff2aplot: warning on stderr) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-06-15 18:40 +0200
  Processed: gffread: autopkgtest needs update for new version of  gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-06-17 17:40 +0200
  Processed: Re: Bug#962553: gffread: autopkgtest needs update for  new version of gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-07-05 19:10 +0200
  Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Adrian Bunk <bunk@debian.org> - 2020-07-06 11:10 +0200
    Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Andreas Tille <tille@debian.org> - 2020-07-21 12:30 +0200
  Processed: Re: Bug#962553: gffread: autopkgtest needs update for  new version of gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-07-06 11:10 +0200
  Processed: Re: Bug#962553: gffread: autopkgtest needs update for  new version of gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-07-27 16:20 +0200
  Processed: Re: Bug#962553: gffread: autopkgtest needs update for  new version of gff2aplot: warning on stderr "Debian Bug Tracking System" <owner@bugs.debian.org> - 2020-07-29 10:10 +0200

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