[Debian-med-packaging] Bug#503367: Bug#503367: Bug#503367: Bug#503367: plink: file conflict with putty-tools

[Luca Capello]

Hi Steffen!

Disclaimer: I'm a biologist [1] and I performed genome-wide analyses.

On Tue, 28 Oct 2008 12:00:02 +0100, Peter Palfrader wrote:
> Steffen Möller schrieb am Dienstag, dem 28. Oktober 2008:
>> To summarise things up: the renaming of the executable of plink to
>> snplink renders the plink package inferior to a manual installation of
>> plink under the proper name.

From a *very* quick read of the plink webpage [2], I understand that
plink mainly deals with SNPs [3].  Thus I don't see the rename as
something inferior, on the contrary it helps better understanding what
the binary does [4].

>> What I'll do now unless I hear some objections that I am mentally
>> prepared to follow: I'll prepare the new version, add the conflict to
>> debian/control to close 503367 (won't fix) and herewith truly
>> apologize for all these emails.
>
> The packages provide different functionality.  They should therefore not
> conflict.
[...]
> Tho I think that putty being the more senior one should have the right
> of the name and not be forced to rename its binaries.

Fully ACK, on both sentences.

FWIW, according to [5], plink has been included in PuTTY since version
beta 0.50 (released 2000/10/16).  The oldest Debian version I could find
is 0.57-1 (2005/03/13), which already contains /usr/bin/plink.

Thx, bye,
Gismo / Luca

Footnotes: 
[1] http://www.unige.ch/irlab
[2] http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml
[3] http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism
[4] I agree that for someone not in genetics this is not true
[5] http://www.chiark.greenend.org.uk/~sgtatham/putty/changes.html
[6] http://snapshot.debian.net/putty
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