Debian Bug report logs - #909714
gff2aplot: Please provide autopkgtest

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: gff2aplot: Please provide autopkgtest

Date: Thu, 27 Sep 2018 08:08:09 +0200

Package: gff2aplot
Severity: minor
Tags: newcomer

Please provide autopkgtest for this package.

-- System Information:
Debian Release: 9.5
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.9.0-6-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages gff2aplot depends on:
ii  libc6  2.24-11+deb9u3
ii  perl   5.24.1-3+deb9u4

gff2aplot recommends no packages.

Versions of packages gff2aplot suggests:
pn  gff2ps                           <none>
ii  ghostscript [postscript-viewer]  9.20~dfsg-3.2+deb9u5

Message #12 received at 909714@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: 909714@bugs.debian.org

Subject: Re: gff2aplot: Please provide autopkgtest

Date: Mon, 10 Dec 2018 13:05:57 +0100

Control: tags -1 pending

I wrote an autopkgtest which uncovered actual bugs in the software.  One
was (hopefully - reviews welcome) fixed[1]

The test suite exposes some other errors - the output is

cp: cannot stat 'taf6.mmhs.genomic.tblastx.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.tblastx.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
cp: cannot stat 'taf6.mmhs.genomic.tblastx.aplot.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.tblastx.aplot.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
cp: cannot stat 'taf6.mmhs.genomic.blastn.aplot_conf.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.blastn.aplot_conf.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
cp: cannot stat 'taf6.mmhs.genomic.tblastx.aplot_conf.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.tblastx.aplot_conf.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
cp: cannot stat 'taf6.mmhs.genomic.blast.merge.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.blast.merge.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
cp: cannot stat 'taf6.mmhs.genomic.blast.merge_conf.png': No such file or directory
mogrify: unable to open image `taf6.mmhs.genomic.blast.merge_conf.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
'taf6.mmhs.genomic.blastn.png' -> 'taf6.mmhs.genomic.blastn.s.png'
'taf6.mmhs.genomic.blastn.aplot.png' -> 'taf6.mmhs.genomic.blastn.aplot.s.png'
Some errors were found in logfiles
taf6.mmhs.genomic.blast.merge.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 1737, <THIS> line 12.
taf6.mmhs.genomic.blast.merge_conf.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 1737.
taf6.mmhs.genomic.blastn.aplot.log:Redundant argument in sprintf at /usr/bin/gff2aplot line 3674.
taf6.mmhs.genomic.blastn.aplot.log:Use of uninitialized value $_[1] in string at /usr/bin/gff2aplot line 3734, <THIS> line 1.
taf6.mmhs.genomic.blastn.aplot_conf.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 1737, <THIS> line 12.
taf6.mmhs.genomic.blastn.log:Redundant argument in sprintf at /usr/bin/gff2aplot line 3674.
taf6.mmhs.genomic.blastn.log:Use of uninitialized value $_[1] in string at /usr/bin/gff2aplot line 3734, <THIS> line 1.
taf6.mmhs.genomic.tblastx.aplot.log:Redundant argument in sprintf at /usr/bin/gff2aplot line 3674.
taf6.mmhs.genomic.tblastx.aplot.log:Use of uninitialized value $_[1] in string at /usr/bin/gff2aplot line 3734, <THIS> line 1.
taf6.mmhs.genomic.tblastx.aplot.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 2934.
taf6.mmhs.genomic.tblastx.aplot_conf.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 1737, <THIS> line 12.
taf6.mmhs.genomic.tblastx.aplotgff.log:Can't open taf6.mmhs.genomic.tblastx: No such file or directory at /usr/bin/parseblast line 889.
taf6.mmhs.genomic.tblastx.log:Redundant argument in sprintf at /usr/bin/gff2aplot line 3674.
taf6.mmhs.genomic.tblastx.log:Use of uninitialized value $_[1] in string at /usr/bin/gff2aplot line 3734, <THIS> line 1.
taf6.mmhs.genomic.tblastx.log:Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 2934.
PostScript file ./taf6.mmhs.genomic.blast.merge.ps has zero bytes.
PostScript file ./taf6.mmhs.genomic.tblastx.aplot.ps has zero bytes.
PostScript file ./taf6.mmhs.genomic.blast.merge_conf.ps has zero bytes.
PostScript file ./taf6.mmhs.genomic.tblastx.ps has zero bytes.
PostScript file ./taf6.mmhs.genomic.tblastx.aplot_conf.ps has zero bytes.
PostScript file ./taf6.mmhs.genomic.blastn.aplot_conf.ps has zero bytes.
convert: unable to open image `*.s.png': No such file or directory @ error/blob.c/OpenBlob/2874.
convert: image file does not contain any image data `*.s.png' @ error/vid.c/ReadVIDImage/208.
convert: no images defined `splicesites.summary.png' @ error/convert.c/ConvertImageCommand/3258.

This should be fixed before uploading.

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/gff2aplot/blob/master/debian/patches/perl_5.28.patch

-- 
http://fam-tille.de

Message #15 received at 890789-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 890789-close@bugs.debian.org

Subject: Bug#890789: fixed in gff2aplot 2.0-11

Date: Wed, 30 Jan 2019 13:34:09 +0000

Source: gff2aplot
Source-Version: 2.0-11

We believe that the bug you reported is fixed in the latest version of
gff2aplot, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 890789@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated gff2aplot package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Wed, 30 Jan 2019 14:12:34 +0100
Source: gff2aplot
Binary: gff2aplot
Architecture: source
Version: 2.0-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 gff2aplot  - pair-wise alignment-plots for genomic sequences in PostScript
Closes: 890789 909714
Changes:
 gff2aplot (2.0-11) unstable; urgency=medium
 .
   * README files in examples are actually scripts - fix PATH to gff2aplot
   * Add autopkgtest
     Closes: #890789, #909714
   * Fix issue with Perl 5.28
   * Fix definition of CP in upstream makefile
   * Try hard to make sprint buffers have proper size
   * Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends)
   * Fix README used as shell script for testing
   * hardening=+all
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 bfc6d2fd17774fd1d323cf4b23e7d1f70ddfa873 19852 gff2aplot_2.0-11.debian.tar.xz
Checksums-Sha256:
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 a3ed0beb0134981b88997d7f4bafc09f25b7b1075260bb24c8331b1d77edaa84 19852 gff2aplot_2.0-11.debian.tar.xz
Files:
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Message #20 received at 909714-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 909714-close@bugs.debian.org

Subject: Bug#909714: fixed in gff2aplot 2.0-11

Date: Wed, 30 Jan 2019 13:34:09 +0000

Source: gff2aplot
Source-Version: 2.0-11

We believe that the bug you reported is fixed in the latest version of
gff2aplot, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 909714@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated gff2aplot package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Wed, 30 Jan 2019 14:12:34 +0100
Source: gff2aplot
Binary: gff2aplot
Architecture: source
Version: 2.0-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 gff2aplot  - pair-wise alignment-plots for genomic sequences in PostScript
Closes: 890789 909714
Changes:
 gff2aplot (2.0-11) unstable; urgency=medium
 .
   * README files in examples are actually scripts - fix PATH to gff2aplot
   * Add autopkgtest
     Closes: #890789, #909714
   * Fix issue with Perl 5.28
   * Fix definition of CP in upstream makefile
   * Try hard to make sprint buffers have proper size
   * Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends)
   * Fix README used as shell script for testing
   * hardening=+all
Checksums-Sha1:
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 bfc6d2fd17774fd1d323cf4b23e7d1f70ddfa873 19852 gff2aplot_2.0-11.debian.tar.xz
Checksums-Sha256:
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 a3ed0beb0134981b88997d7f4bafc09f25b7b1075260bb24c8331b1d77edaa84 19852 gff2aplot_2.0-11.debian.tar.xz
Files:
 09e4d88e63d7be64b3a894c4867ec4b6 2082 science optional gff2aplot_2.0-11.dsc
 a86186908f5484b79c37945c64e86db2 19852 science optional gff2aplot_2.0-11.debian.tar.xz

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