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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 Graham Inggs <ginggs@debian.org> - 2020-06-17 17:40 +0200
    Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Adrian Bunk <bunk@debian.org> - 2020-07-05 19:10 +0200
      Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Graham Inggs <ginggs@debian.org> - 2020-07-06 01:10 +0200
        Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Pranav Ballaney <ballaneypranav@gmail.com> - 2020-07-27 16:20 +0200
          Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr Graham Inggs <ginggs@debian.org> - 2020-07-29 10:10 +0200

#1014224 — Bug#962553: gffread: autopkgtest needs update for new version of gff2aplot: warning on stderr

Control: reopen -1

Now it fails in a different way:

autopkgtest [11:10:15]: test run-tests:  - - - - - - - - - - results -
- - - - - - - - -
run-tests            FAIL stderr:
/tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
line 109:  8512 Segmentation fault      gffread ${gff} > /dev/null
autopkgtest [11:10:15]: test run-tests:  - - - - - - - - - - stderr -
- - - - - - - - -
/tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
line 109:  8512 Segmentation fault      gffread ${gff} > /dev/null
/tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
line 109:  8514 Segmentation fault      gffread ${gff} > /dev/null

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#1016643

Control: reassign -1 src:gff2aplot
Control: close -1 2.0-13

On Wed, Jun 17, 2020 at 05:39:43PM +0200, Graham Inggs wrote:
> Control: reopen -1
> 
> Now it fails in a different way:
> 
> autopkgtest [11:10:15]: test run-tests:  - - - - - - - - - - results -
> - - - - - - - - -
> run-tests            FAIL stderr:
> /tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
> line 109:  8512 Segmentation fault      gffread ${gff} > /dev/null
> autopkgtest [11:10:15]: test run-tests:  - - - - - - - - - - stderr -
> - - - - - - - - -
> /tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
> line 109:  8512 Segmentation fault      gffread ${gff} > /dev/null
> /tmp/autopkgtest-lxc.cerfkec6/downtmp/build.2n1/src/debian/tests/run-tests:
> line 109:  8514 Segmentation fault      gffread ${gff} > /dev/null

This is #962550.

cu
Adrian

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#1016705

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.

Regards
Graham

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#1019479

[Multipart message — attachments visible in raw view] — view raw

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@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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#1019672

Control: reassign -1 src:gffread 0.11.8-1
Control: severity -1 serious
Control: tags -1 - moreinfo unreproducible

Hi

gff2aplot 2.0-13 migrated to testing and now causes gffread's
autopkgtests to fail there [1].
I'm reassigning this bug accordingly.

Please see the results of the recent migration-reference/0 run, dated
2020-07-28 18:10:16 UTC.
I've copied what I hope is the relevant part below.

Regards
Graham


[1] https://ci.debian.net/packages/g/gffread/testing/amd64/


/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.gff:
is okay.
/usr/share/spades/test_dataset/genes_1K.gff: is okay.
/usr/share/spades/test_dataset/operons_1K.gff: is okay.
autopkgtest [18:10:14]: test run-tests: -----------------------]
autopkgtest [18:10:14]: test run-tests:  - - - - - - - - - - results -
- - - - - - - - -
run-tests            FAIL stderr:
/tmp/autopkgtest-lxc.msyyr56h/downtmp/build.f2j/src/debian/tests/run-tests:
line 109:  8521 Segmentation fault      gffread ${gff} > /dev/null
autopkgtest [18:10:14]: test run-tests:  - - - - - - - - - - stderr -
- - - - - - - - -
/tmp/autopkgtest-lxc.msyyr56h/downtmp/build.f2j/src/debian/tests/run-tests:
line 109:  8521 Segmentation fault      gffread ${gff} > /dev/null
/tmp/autopkgtest-lxc.msyyr56h/downtmp/build.f2j/src/debian/tests/run-tests:
line 109:  8523 Segmentation fault      gffread ${gff} > /dev/null
autopkgtest [18:10:14]: @@@@@@@@@@@@@@@@@@@@ summary
run-tests            FAIL stderr:
/tmp/autopkgtest-lxc.msyyr56h/downtmp/build.f2j/src/debian/tests/run-tests:
line 109:  8521 Segmentation fault      gffread ${gff} > /dev/null

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