Your message dated Tue, 26 Jun 2018 02:15:44 +0000
with message-id <[email protected]>
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 [email protected]
immediately.)
--
902364: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902364
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: ncbi-data,ncbi-rrna-data
Version: 6.1.20170106-2
Severity: serious
User: [email protected]
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
Description: application/gzip
--- End Message ---
--- 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (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 [email protected])
-----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
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
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-----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=tgex
-----END PGP SIGNATURE-----
--- End Message ---
