Your message dated Sun, 22 Sep 2013 06:03:26 +0000
with message-id <[email protected]>
and subject line Bug#722910: fixed in bioperl 1.6.922-1
has caused the Debian Bug report #722910,
regarding libbio-perl-perl: incorporated some perl modules from grinder
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
722910: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=722910
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: grinder,libbio-perl-perl
Version: 1.6.920-1
Severity: serious
User: [email protected]
Usertags: edos-file-overwrite
Architecture: amd64
Distribution: sid
Hi,
automatic installation tests of packages that share a file and at the
same time do not conflict by their package dependency relationships has
detected the following problem:
Selecting previously unselected package grinder.
Unpacking grinder (from .../grinder_0.5.3-2_all.deb) ...
dpkg: error processing /var/cache/apt/archives/grinder_0.5.3-2_all.deb
(--unpack):
trying to overwrite '/usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm.gz',
which is also in package libbio-perl-perl 1.6.920-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
This is a serious bug as it makes installation fail, and violates
sections 7.6.1 and 10.1 of the policy. An optimal solution would
consist in only one of the packages installing that file, and renaming
or removing the file in the other package. Depending on the
circumstances you might also consider Replace relations or file
diversions. If the conflicting situation cannot be resolved then, as a
last resort, the two packages have to declare a mutual
Conflict. Please take into account that Replaces, Conflicts and
diversions should only be used when packages provide different
implementations for the same functionality.
Here is a list of files that are known to be shared by both packages
(according to the Contents file for sid/amd64, which may be
slightly out of sync):
usr/share/man/man3/Bio::DB::IndexedBase.3pm.gz
usr/share/man/man3/Bio::Seq::SimulatedRead.3pm.gz
usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm.gz
usr/share/man/man3/Bio::SeqFeature::SubSeq.3pm.gz
usr/share/man/man3/Bio::Tools::AmpliconSearch.3pm.gz
usr/share/perl5/Bio/DB/IndexedBase.pm
usr/share/perl5/Bio/Seq/SimulatedRead.pm
usr/share/perl5/Bio/SeqFeature/Amplicon.pm
usr/share/perl5/Bio/SeqFeature/SubSeq.pm
usr/share/perl5/Bio/Tools/AmpliconSearch.pm
This bug is assigned to both packages. If you, the maintainers of
the two packages in question, have agreed on which of the packages will
resolve the problem please reassign the bug to that package. You may
also register in the BTS that the other package is affected by the bug.
Cheers,
Andreas
PS: for more information about the detection of file overwrite errors
of this kind see http://edos.debian.net/file-overwrites/.
grinder=0.5.3-2_libbio-perl-perl=1.6.920-1.log.gz
Description: GNU Zip compressed data
--- End Message ---
--- Begin Message ---
Source: bioperl
Source-Version: 1.6.922-1
We believe that the bug you reported is fixed in the latest version of
bioperl, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <[email protected]> (supplier of updated bioperl 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 22 Sep 2013 13:39:48 +0900
Source: bioperl
Binary: bioperl libbio-perl-perl
Architecture: source all
Version: 1.6.922-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Charles Plessy <[email protected]>
Description:
bioperl - Perl tools for computational molecular biology
libbio-perl-perl - BioPerl core perl modules
Closes: 722910
Changes:
bioperl (1.6.922-1) unstable; urgency=low
.
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore.
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Files:
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bioperl_1.6.922-1.debian.tar.gz
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bioperl_1.6.922-1_all.deb
b15856c40706c0efdbd47c5d387bf255 4752426 perl optional
libbio-perl-perl_1.6.922-1_all.deb
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