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

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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

#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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#279748 — Processed: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> affects -1 src:gff2aplot
Bug #962553 [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Added indication that 962553 affects src:gff2aplot

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#280061 — Bug#962553: Bugfix: Patched gff2aplot

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Hi,
This error occurs because gffread complains about tabs in comments for some
reason, even though GFF parsers are supposed to ignore all the lines that
start with #. Since these lines are human-readable comments anyway,
replacing tabs with spaces seems like the easiest fix. I've patched
gff2aplot and autopkgtests pass now. Please take a look.

Regards,
Pranav
ᐧ

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#280073 — Bug#962553: marked as done (gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr)

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Your message dated Mon, 15 Jun 2020 16:33:28 +0000
with message-id <E1jks36-0005bg-Qg@fasolo.debian.org>
and subject line Bug#962553: fixed in gff2aplot 2.0-13
has caused the Debian Bug report #962553,
regarding gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#280181 — Processed: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> reopen -1
Bug #962553 {Done: Pranav Ballaney <ballaneypranav@gmail.com>} [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions gff2aplot/2.0-13.

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#281434 — Processed: Re: Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> reassign -1 src:gff2aplot
Bug #962553 [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Bug reassigned from package 'src:gffread' to 'src:gff2aplot'.
No longer marked as found in versions gffread/0.11.8-1.
Ignoring request to alter fixed versions of bug #962553 to the same values previously set
> close -1 2.0-13
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Marked as fixed in versions gff2aplot/2.0-13.
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Marked Bug as done

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#281476

Control: reopen -1

On Mon, Jul 06, 2020 at 01:07:22AM +0200, Graham Inggs wrote:
> Hi Adrian
> 
> On Sun, 5 Jul 2020 at 19:02, Adrian Bunk <bunk@debian.org> wrote:
> > This is #962550.
> 
> Are you sure?
> 
> The failing test was with ligclib1 0.11.8-1 from testing and gff2aplot
> 2.0-13 from unstable.

Right you are, thanks for noticing my mistake.

The actual problem is:
Due to the dh compat bump in gff2aplot the gffread autopkgtest runs
additional tests, and on two of these gffread is segfaulting.

> Regards
> Graham

cu
Adrian

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#282450

Hi Pranav,

On Mon, Jul 06, 2020 at 12:06:06PM +0300, Adrian Bunk wrote:
> 
> The actual problem is:
> Due to the dh compat bump in gff2aplot the gffread autopkgtest runs
> additional tests, and on two of these gffread is segfaulting.

I've checked the debdiff of the two binary packages in question
which are affected by the debhelper compat bump:

$ debdiff gff2aplot_2.0-11_amd64.deb gff2aplot_2.0-12_amd64.deb
[The following lists of changes regard files as different if they have
different names, permissions or owners.]

Files in second .deb but not in first
-------------------------------------
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/README
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.tblastx.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs.fa
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/kk.sim
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/mm.fa
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.AG.hs-mm.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.GT.hs-mm.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.hs.gb
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.mm.gb
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/README
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/README
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.hs.gene.gb
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mm.gene.gb
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn.full.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.tblastx.aplot.gff
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.tblastx.gff

Files in first .deb but not in second
-------------------------------------
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/README.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.tblastx.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/hs.fa.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/kk.sim.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/mhcregion/mm.fa.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.AG.hs-mm.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.GT.hs-mm.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.hs.gb.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/KCRB.mm.gb.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/splice_sites/README.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/README.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.hs.gene.gb.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mm.gene.gb.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn.full.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.tblastx.aplot.gff.gz
-rw-r--r--  root/root   /usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.tblastx.gff.gz

Control files: lines which differ (wdiff format)
------------------------------------------------
Installed-Size: [-647-] {+1451+}
Version: [-2.0-11-] {+2.0-12+}


So the files are not compressed now any more.  Could you have
a look at the consequences this has on the test in gffread?

Kind regards

        Andreas.

-- 
http://fam-tille.de

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#281477 — Processed: Re: Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> reopen -1
Bug #962553 {Done: Adrian Bunk <bunk@debian.org>} [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions gff2aplot/2.0-13.

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#283080 — Processed: Re: Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> tags -1 moreinfo
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Added tag(s) moreinfo.
> severity -1 important
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Severity set to 'important' from 'serious'
> tags -1 unreproducible
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Added tag(s) unreproducible.

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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#283207 — Processed: Re: Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Processing control commands:

> reassign -1 src:gffread 0.11.8-1
Bug #962553 [src:gff2aplot] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Bug reassigned from package 'src:gff2aplot' to 'src:gffread'.
Ignoring request to alter found versions of bug #962553 to the same values previously set
Ignoring request to alter fixed versions of bug #962553 to the same values previously set
Bug #962553 [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Marked as found in versions gffread/0.11.8-1.
> severity -1 serious
Bug #962553 [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Severity set to 'serious' from 'important'
> tags -1 - moreinfo unreproducible
Bug #962553 [src:gffread] gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr
Removed tag(s) moreinfo and unreproducible.

-- 
962553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962553
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

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