Your message dated Tue, 10 Jul 2018 15:04:28 +0000 with message-id <e1fcubo-000itu...@fasolo.debian.org> and subject line Bug#903456: fixed in libbio-tools-phylo-paml-perl 1.7.3-2 has caused the Debian Bug report #903456, regarding 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 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.) -- 903456: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=903456 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: libbio-tools-phylo-paml-perl Version: 1.7.3-1 Severity: serious User: debian...@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
libbio-perl-perl=1.7.1-2_libbio-tools-phylo-paml-perl=1.7.3-1.log.gz
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--- Begin Message ---Source: libbio-tools-phylo-paml-perl Source-Version: 1.7.3-2 We believe that the bug you reported is fixed in the latest version of libbio-tools-phylo-paml-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 903...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. David Miguel Susano Pinto <carandraug+...@gmail.com> (supplier of updated libbio-tools-phylo-paml-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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Tue, 10 Jul 2018 13:02:50 +0100 Source: libbio-tools-phylo-paml-perl Binary: libbio-tools-phylo-paml-perl Architecture: source Version: 1.7.3-2 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group <pkg-perl-maintain...@lists.alioth.debian.org> Changed-By: David Miguel Susano Pinto <carandraug+...@gmail.com> Closes: 903456 Description: libbio-tools-phylo-paml-perl - Bioperl interface to the PAML suite Changes: libbio-tools-phylo-paml-perl (1.7.3-2) unstable; urgency=medium . * This package also breaks/replaces bioperl << 1.7.2 Closes: #903456 * Bump Standards-Version to 4.1.5 (no changes needed) Checksums-Sha1: ba6c981d797207321845faf810bf93e101fd6e88 2465 libbio-tools-phylo-paml-perl_1.7.3-2.dsc ce85d06455016d3669df5b36c61bf99a4c11f7d5 2436 libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz Checksums-Sha256: 53aa9260f82b79f43f6303229e947f2f8cbfc725af28d31d23d632aa31d67b28 2465 libbio-tools-phylo-paml-perl_1.7.3-2.dsc 9312c2b696ee512dce8495ea1a0a8da5d7c04b74af4a088c7ac7c36b17b361d6 2436 libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz Files: 511cf173d069028db579b289dcd941dd 2465 science optional libbio-tools-phylo-paml-perl_1.7.3-2.dsc e4886bb10e001031d8c2fe6545e1ac99 2436 science optional libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEE0eExbpOnYKgQTYX6uzpoAYZJqgYFAltExElfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEQx RTEzMTZFOTNBNzYwQTgxMDREODVGQUJCM0E2ODAxODY0OUFBMDYACgkQuzpoAYZJ qgaAWg//VQy7/ZGUoCg0vRmInH4Crl0Z+8IGYCH2MA1GalERZ+a18ZucmzyRYjZo hiU0AHgxjNl23lOf1WNfLs5sYpmcvt8No7F+8BkQdxzuiKoF0vkZ0ULqbLn03jQD iKeZdqnDPsraoWKUFIbEZgBHLbmDGaAP3GUw8mf5olF7b+ZJV1/KBirmHTtBvzkS PAdfKdDCisGYwyciqUmh6NYFt2ezktFDq//ZoOrzD1r/KCmr6E0n3TYCjbE70WYX 1B2I1sSmNQvjtodPgTaZik6JP7rxumdL0zRpZbwruRUys5AyWpA5PNKBu80asvcQ fNZT/KhBxIOXZrmrYb7FvQdRzX/POqk4idCbTEdaXR9Gv1dqLJl6DIOFLcZgIzqv YUeJaQADVv0Ix3fPAdqhJgRHg+6kZA3ExglfGaEyOEyR108kxiVD06ViLDhcaaJQ 9ufs/gLy4J0OyRMKPvyHAAreHXby3vzx48hLRRkItp4V0aOH4+bRQQXA+SnU4yMf DME3MACC4/gk3iGbvQqjXGmkM64MFQN/fMjlZUdbheDTBatwsdWoxJ6My4p0HIAn 869j23zLlz/w7OiTvZuSIEwPWAgEe8e5BUue1YvgGpBYr/Jpup4eiNy3Skl4gCNM mLjXbKI2m2rZ6ukgkzr2PcWYwRyeXl5khDEbazx8KRX4IYRcSqM= =K59d -----END PGP SIGNATURE-----
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