[Debian-med-packaging] Bug#737913: exonerate and dnaclust: error when trying to install together

[Ralf Treinen]

Package: dnaclust,exonerate
Version: dnaclust/3-1
Version: exonerate/2.2.0-6
Severity: serious
User: treinen at debian.org
Usertags: edos-file-overwrite

Date: 2014-02-06
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 libboost-program-options1.54.0:amd64.
(Reading database ... 10921 files and directories currently installed.)
Preparing to unpack .../libboost-program-options1.54.0_1.54.0-4+b1_amd64.deb ...
Unpacking libboost-program-options1.54.0:amd64 (1.54.0-4+b1) ...
Selecting previously unselected package libffi6:amd64.
Preparing to unpack .../libffi6_3.0.13-12_amd64.deb ...
Unpacking libffi6:amd64 (3.0.13-12) ...
Selecting previously unselected package libglib2.0-0:amd64.
Preparing to unpack .../libglib2.0-0_2.36.4-1_amd64.deb ...
Unpacking libglib2.0-0:amd64 (2.36.4-1) ...
Selecting previously unselected package dnaclust.
Preparing to unpack .../dnaclust_3-1_amd64.deb ...
Unpacking dnaclust (3-1) ...
Selecting previously unselected package exonerate.
Preparing to unpack .../exonerate_2.2.0-6_amd64.deb ...
Unpacking exonerate (2.2.0-6) ...
dpkg: error processing archive /var/cache/apt/archives/exonerate_2.2.0-6_amd64.deb (--unpack):
 trying to overwrite '/usr/bin/fastasort', which is also in package dnaclust 3-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Processing triggers for man-db (2.6.6-1) ...
Errors were encountered while processing:
 /var/cache/apt/archives/exonerate_2.2.0-6_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)


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/bin/fastasort

This bug has been filed against 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 then
also register in the BTS that the other package is affected by the bug.

-Ralf.

PS: for more information about the detection of file overwrite errors
of this kind see http://edos.debian.net/file-overwrites/.