Your message dated Tue, 26 Jun 2018 02:15:44 +0000 with message-id <e1fxdwc-0007kr...@fasolo.debian.org> and subject line Bug#902364: fixed in ncbi-tools6 6.1.20170106-4 has caused the Debian Bug report #902364, regarding ncbi-data,ncbi-rrna-data: Replaces without Breaks allow invalid partial up/downgrades 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.) -- 902364: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902364 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: ncbi-data,ncbi-rrna-data Version: 6.1.20170106-2 Severity: serious User: debian...@lists.debian.org Usertags: piuparts replaces-without-breaks Hi, during a test with piuparts and DOSE tools I noticed your package causes removal of files that also belong to another package. This is caused by using Replaces without corresponding Breaks. The installation sequence to reproduce this problem is VICTIM=ncbi-data, OFFENDER=ncbi-rrna-data apt-get install $VICTIM/jessie # (1) apt-get install $OFFENDER/stretch apt-get remove $OFFENDER # (2) The list of installed files at points (1) and (2) should be identical, but the following files have disappeared: /usr/share/ncbi/data/Combined16SrRNA.nhr /usr/share/ncbi/data/Combined16SrRNA.nin /usr/share/ncbi/data/Combined16SrRNA.nsq /usr/share/ncbi/data/rRNAstrand.nal This is a serious bug violating policy 7.6, see https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces and also see the footnote that describes this incorrect behavior https://www.debian.org/doc/debian-policy/ (old: footnotes.html#f53) [footnote permalink broken (#879048), search for /To see why/] The $OFFENDER package has the following relationships with $VICTIM: Conflicts: n/a Breaks: n/a Replaces: ncbi-data (<< 6.1.20160908) >From the attached log (scroll to the bottom...): 0m40.2s ERROR: FAIL: After purging files have disappeared: /usr/share/ncbi/data/Combined16SrRNA.nhr owned by: ncbi-rrna-data /usr/share/ncbi/data/Combined16SrRNA.nin owned by: ncbi-rrna-data /usr/share/ncbi/data/Combined16SrRNA.nsq owned by: ncbi-rrna-data /usr/share/ncbi/data/rRNAstrand.nal owned by: ncbi-rrna-data 0m40.2s ERROR: FAIL: After purging files have been modified: /var/lib/dpkg/info/ncbi-data.list not owned Similar effects can be shown with VICTIM and OFFENDER swapped, the affected files in this case are /usr/share/ncbi/data/Combined16SrRNA_2-12-2008.nhr /usr/share/ncbi/data/Combined16SrRNA_2-12-2008.nin /usr/share/ncbi/data/Combined16SrRNA_2-12-2008.nsq Mixing one data file from stretch and one datafile from jessie also means that one set of the moved files is missing. Which is not a problem from dpkg point of view, but perhaps from your application logic. cheers, Andreas
ncbi-data=6.1.20120620-8_ncbi-rrna-data=6.1.20170106-2.log.gz
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--- Begin Message ---Source: ncbi-tools6 Source-Version: 6.1.20170106-4 We believe that the bug you reported is fixed in the latest version of ncbi-tools6, 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 902...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-tools6 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: SHA256 Format: 1.8 Date: Mon, 25 Jun 2018 21:36:10 -0400 Source: ncbi-tools6 Binary: libncbi6 libncbi6-dev ncbi-data ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 libvibrant6b libvibrant6-dev Architecture: source Version: 6.1.20170106-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Description: libncbi6 - NCBI libraries for biology applications libncbi6-dev - NCBI libraries for biology applications (development files) libvibrant6-dev - NCBI libraries for graphic biology applications (development file libvibrant6b - NCBI libraries for graphic biology applications ncbi-data - Platform-independent data for the NCBI toolkit ncbi-rrna-data - large rRNA BLAST databases distributed with the NCBI toolkit ncbi-tools-bin - NCBI libraries for biology applications (text-based utilities) ncbi-tools-x11 - NCBI libraries for biology applications (X-based utilities) Closes: 902364 Changes: ncbi-tools6 (6.1.20170106-4) unstable; urgency=medium . * debian/compat: Advance to Debhelper 11. * debian/control: - Mark *-data reshuffling with Breaks, not just Replaces. (Closes: #902364.) - Build-Depends: Advance to debhelper (>= 11~). * debian/copyright: Fix years (packaging through 2018, upstream through 2017). Checksums-Sha1: 229140ae1c153942262457dc35f57316fd00de71 2784 ncbi-tools6_6.1.20170106-4.dsc 4b0823fa34fa03ec83a713438030a581dce4f51c 1508576 ncbi-tools6_6.1.20170106-4.debian.tar.xz Checksums-Sha256: b2f6765a1c6574183901887ee2662e2aca43d373d3556d48ed05af49d635fe3d 2784 ncbi-tools6_6.1.20170106-4.dsc 95ee25df0f94fe854c757c9199c58964e323aa78a20a9ec49af763bb526bd616 1508576 ncbi-tools6_6.1.20170106-4.debian.tar.xz Files: 30758dea03804c5662db676a3bd4c735 2784 libdevel optional ncbi-tools6_6.1.20170106-4.dsc 4008f4a1df1b01e8bd6d0b63b5e41fab 1508576 libdevel optional ncbi-tools6_6.1.20170106-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAlsxm10ACgkQHnCRsfFK ZKLb0g//Ss7WtTzmNGFX5eXVjPYIDC9xDAxOHaeB35ZGeH43ty5/eR9Vv6mVWgCK 11h8BMZfTlw/kx9EWbUtkUR69KVXJW0yakVGygR4UncoqVo6QiiGOXzdTosGol76 xHg+ytAI1nQ9Mcs2Jk7ho4wqiMPEBRqJjI3vjx5v2T3tOYJO3fycFJ0L0Ab5btly yFQ0iYcMrU2EnBqXB5r+j/+8fA1Kd84cZQkp6xuCl+BILQWRZEzD3g3tEHf5RCtJ 1ALrfGq9aXSpk6XRx1I05Bcka53snq9Xh6fjbDb6ftiuDMSzr5VfSDPc7J39j3zo DXmQQYPYhSUoYkVTvwst4UtNugXRKVBUrSBTf7Hl7HXuT3tch1kJKYM/E1HDN/2B uTHUAxaF9mHpMOIfANPRh60LMXJn+AnY8fnyxIgZTB3sDcw+OnTqpOxxFxGd1AMj RT3bd6xJbbVjD1tat0a+VTMuEfRXqgFzt1Y+D3Qqf2xt3LzdqCrjfF2xJkIT9x+9 lTtmgeSOC+TCYBUp7USDQ6bCU84Jc8aGrzj3m6IrXF1zLz4CsJSRHG2jmOM0nCiR AKPlRMXcFEX2I3C8z1okKzF76k4E+dCLxon6uC8snOyge5PHMk7AbWb9w7/AoOSw cJeXkelmwU9v62uCLT3ywIDqxcbijfgDA9uKaTqQ11rtF9lkY9k= =tgex -----END PGP SIGNATURE-----
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