Your message dated Fri, 13 Sep 2013 07:48:01 +0000 with message-id <e1vko6j-00068e...@franck.debian.org> and subject line Bug#722650: fixed in grinder 0.5.3-3 has caused the Debian Bug report #722650, regarding grinder,libbio-perl-perl: error when trying to install together 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 ow...@bugs.debian.org immediately.) -- 722650: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=722650 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: grinder,libbio-perl-perl Version: 1.6.920-1 Severity: serious User: trei...@debian.org 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
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--- Begin Message ---Source: grinder Source-Version: 0.5.3-3 We believe that the bug you reported is fixed in the latest version of grinder, 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 722...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated grinder 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Fri, 13 Sep 2013 08:25:06 +0200 Source: grinder Binary: grinder Architecture: source all Version: 0.5.3-3 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: grinder - Versatile omics shotgun and amplicon sequencing read simulator Closes: 722650 Changes: grinder (0.5.3-3) unstable; urgency=low . * debian/rules: - Move more duplicates from libbio-perl-perl out of the way Closes: #722650 Remark: It seems libbio-perl-perl is integrating actively code from grinder and includes it into their distribution. Finally now are all modules from the Bio directory integrated into BioPerl. - Obtain version from changelog instead of setting it manually (which is in danger to age without noticing) * debian/control: anonscm in Vcs fields Checksums-Sha1: 9a010af22a7297ae2055b132bbacde691174c0ba 1436 grinder_0.5.3-3.dsc d3fd410ff630049d2d510d593476b2ddae6d3efb 4142 grinder_0.5.3-3.debian.tar.gz fc784e20b8053a847d3853ea0027ce5d958ea13c 81586 grinder_0.5.3-3_all.deb Checksums-Sha256: 681c2ca8f889edd120b3beb830e55c26e1628460aab4890edb6406b5815f80cc 1436 grinder_0.5.3-3.dsc e9a1ae7540784fac7fb6178fd9e483956f6b56e8f5804dffeb86d2566a0c8cb8 4142 grinder_0.5.3-3.debian.tar.gz 7794a4c63776e590731880be6396fa08bc6eb6670b7f6d63ba4b585084f3f52b 81586 grinder_0.5.3-3_all.deb Files: c43d698a301421446b882eeb14b35d01 1436 science optional grinder_0.5.3-3.dsc 062e22465c8e014e549bc4b3ae193f4d 4142 science optional grinder_0.5.3-3.debian.tar.gz bec9500c7234a59dae50c034a591cd17 81586 science optional grinder_0.5.3-3_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) iEYEARECAAYFAlIywSQACgkQYDBbMcCf01qHVQCgh3t1Di9ucOsTQ0OfZMjXqyf4 2YgAoKBO+Ya+iP1LmE3oD0O3NUgHRRnn =3Yf2 -----END PGP SIGNATURE-----
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