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Bug#984477: marked as done (libbio-variation-perl: missing Breaks+Replaces: bioperl (<< 1.7.3))

Your message dated Thu, 04 Mar 2021 13:18:23 +0000
with message-id <E1lHnrz-000Gcu-JJ@fasolo.debian.org>
and subject line Bug#984477: fixed in libbio-variation-perl 1.7.5-2
has caused the Debian Bug report #984477,
regarding libbio-variation-perl: missing Breaks+Replaces: bioperl (<< 1.7.3)
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
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-- 
984477: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984477
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: libbio-variation-perl
Version: 1.7.5-1
Severity: serious
User: debian-qa@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'buster'.
It installed fine in 'buster', then the upgrade to 'bullseye' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#overwriting-files-and-replacing-packages-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libbio-variation-perl.
  Preparing to unpack .../048-libbio-variation-perl_1.7.5-1_all.deb ...
  Unpacking libbio-variation-perl (1.7.5-1) ...
  dpkg: error processing archive /tmp/apt-dpkg-install-eyjeT8/048-libbio-variation-perl_1.7.5-1_all.deb (--unpack):
   trying to overwrite '/usr/bin/bp_flanks', which is also in package bioperl 1.7.2-3
  dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)

IIRC bioperl 1.7.3 is the version that got split up into several packages,
therefore the existing
  Breaks+Replaces: libbio-perl-perl (<= 1.7.2)
are also insufficiently versioned (should be (<< 1.7.3) as well).

cheers,

Andreas

Attachment: bioperl-run_1.7.3-6.log.gz
Description: application/gzip


--- End Message ---
--- Begin Message --- 
Source: libbio-variation-perl
Source-Version: 1.7.5-2
Done: Andreas Tille <tille@debian.org>

We believe that the bug you reported is fixed in the latest version of
libbio-variation-perl, 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 984477@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 libbio-variation-perl 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: SHA512

Format: 1.8
Date: Thu, 04 Mar 2021 13:55:37 +0100
Source: libbio-variation-perl
Architecture: source
Version: 1.7.5-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 984477
Changes:
 libbio-variation-perl (1.7.5-2) unstable; urgency=medium
 .
   * Team upload.
   * Fix maintainer address
   * Add debian/salsa-ci.yml
   * Breaks+Replaces: bioperl (<< 1.7.3)
     Closes: #984477
Checksums-Sha1:
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 da8ec9b9f37993aebea0805f57b8a6b1f3328f3e 2052 libbio-variation-perl_1.7.5-2.debian.tar.xz
 e497eedd383a5c47cf3ecd69f0c7d5a1129fbafe 7420 libbio-variation-perl_1.7.5-2_amd64.buildinfo
Checksums-Sha256:
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 80892316d8c5916336dae5c00b71cd4efcaa36e665a44a4d2529b31af77f4ed4 2052 libbio-variation-perl_1.7.5-2.debian.tar.xz
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Files:
 95819385a30bb2c3a9422e585cf669be 2286 perl optional libbio-variation-perl_1.7.5-2.dsc
 a9554a36af420584e21916fae8778dde 2052 perl optional libbio-variation-perl_1.7.5-2.debian.tar.xz
 9eebf28a9a9b33b77653193fe1859cbd 7420 perl optional libbio-variation-perl_1.7.5-2_amd64.buildinfo

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--- End Message ---
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