[Debian-med-packaging] Bug#737913: Scientists please raise your opinion (Was: Bug#737913: exonerate and dnaclust: error when trying to install together)

[Daniel Barker]

Hi Andreas,

In my view, the dnaclust fastasort should be renamed. Exonerate is a
flexible and extremely widely used package. (This is no disrespect to
danclust, which looks useful too. But someone has to be renamed here.)

Incidentally - it's funny that this very file came up as a hypothetical
example of something that might clash, at the sprint.

Thanks,

Daniel

On 07/02/2014 12:57, "Andreas Tille" <andreas at an3as.eu> wrote:

>Hi,
>
>as you can read in the following bug report we need to decide what
>package should provide the binary
>
>   /usr/bin/fastasort
>
>and in what package this should be renamed (including suggestions for a
>new name).  The good thing is that both package are under Debian Med
>maintenance and we are free to decide.
>
>Kind regards
>
>        Andreas.
>
>----- Forwarded message from Ralf Treinen <treinen at free.fr> -----
>
>Date: Thu, 06 Feb 2014 23:40:51 +0100
>From: Ralf Treinen <treinen at free.fr>
>To: submit at bugs.debian.org
>Subject: Bug#737913: exonerate and dnaclust: error when trying to install
>together
>X-Debian-PR-Message: report 737913
>X-Debian-PR-Package: dnaclust,exonerate
>X-Debian-PR-Keywords:
>
>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/.
>
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>ng
>
>
>----- End forwarded message -----
>
>-- 
>http://fam-tille.de
>
>
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>


-- 
Daniel Barker
http://biology.st-andrews.ac.uk/staff/db60
The University of St Andrews is a charity registered in Scotland :
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