[Debian-med-packaging] Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

[Pranav Ballaney]

Control: tags -1 moreinfo
Control: severity -1 important
Control: tags -1 unreproducible

Hi Andreas,
I tried reproducing this bug but all tests simply pass for me, even when I
manually install the specified versions.
The compression doesn't seem to have any effect on the tests for me.

Regards,
Pranav

On Tue, Jul 21, 2020 at 3:46 PM Andreas Tille <tille at debian.org> wrote:

> 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
>
ᐧ
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