Bug#903456: libbio-tools-phylo-paml-perl: fails to upgrade from 'stable' to 'sid' - trying to overwrite /usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm.gz

[Andreas Beckmann]

Package: libbio-tools-phylo-paml-perl
Version: 1.7.3-1
Severity: serious
User: debian-qa at lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'stable'.
It installed fine in 'stable', then the upgrade to 'sid' 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/#overwriting-files-and-replacing-packages-replaces

This test intentionally skipped 'testing' to find file overwrite
problems before packages migrate from 'unstable' to 'testing'.

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

  Selecting previously unselected package libbio-tools-phylo-paml-perl.
  Preparing to unpack .../libbio-tools-phylo-paml-perl_1.7.3-1_all.deb ...
  Unpacking libbio-tools-phylo-paml-perl (1.7.3-1) ...
  dpkg: error processing archive /var/cache/apt/archives/libbio-tools-phylo-paml-perl_1.7.3-1_all.deb (--unpack):
   trying to overwrite '/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm.gz', which is also in package libbio-perl-perl 1.7.1-2
  Errors were encountered while processing:
   /var/cache/apt/archives/libbio-tools-phylo-paml-perl_1.7.3-1_all.deb

  Selecting previously unselected package libbio-tools-phylo-paml-perl.
  Preparing to unpack .../libbio-tools-phylo-paml-perl_1.7.3-1_all.deb ...
  Unpacking libbio-tools-phylo-paml-perl (1.7.3-1) ...
  dpkg: error processing archive /var/cache/apt/archives/libbio-tools-phylo-paml-perl_1.7.3-1_all.deb (--unpack):
   trying to overwrite '/usr/bin/bp_pairwise_kaks', which is also in package bioperl 1.7.1-2
  dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libbio-tools-phylo-paml-perl_1.7.3-1_all.deb

The following files are taken over by libbio-tools-phylo-paml-perl:

  usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm.gz
  usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm.gz
  usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm.gz
  usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm.gz
  usr/share/perl5/Bio/Tools/Phylo/PAML.pm
  usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm
  usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm
  usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm

  usr/bin/bp_pairwise_kaks
  usr/share/man/man1/bp_pairwise_kaks.1p.gz

cheers,

Andreas
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