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

[Andreas Tille]

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