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

[Steffen Möller]

Charles Plessy schrieb:
> Le Tue, Oct 28, 2008 at 09:32:42AM +0200, Teodor a écrit :
>   
>> I still believe it is best to rename 'plink' to 'puttylink' in
>> putty-tools binary package. Anyway, this should be fixed for squeeze
>> since in lenny there is no conflict (plink is not included in lenny).
>>     
>
> Hi all,
>
> Upstream documented the renaming on his website, so I think that that is the
> (happy) end of the story :)
>
>   "Debian users: PLINK is available as a Debian package, see these notes. Note, the
>   executable is named snplink in the Debian plink package."
>
> http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
>   
To me, the renaming to snplink is an exceptionally unfortunate way to
address the name-conflict we experienced. This way, we render Debian
incompatible with scripts distributed in the community and incompatible
with computational grids, too. I am just writing from a grid conference
and plink was indeed referenced on one slide. I don't want either plink
to be renamed, completely following the points brought up Brian and
definitely prefer a conflict between the two plink packages. Those users
who _really_ need both and _really_ need to work with Debian packages
only, they can have a chroot environment for the bioinformatics-plink.
Besides: there is a SNPLINK already:
http://bioinformatics.oxfordjournals.org/cgi/content/full/21/13/3060

The executable in either package should not be renamed. I don't see a
reasonable way around it. The only problem that I originally understood
from skimming over the thread was that Debian packages would be named
equally and I was too busy to wonder for too long how this could be
allowed by the Debian infrastructure. But embarrassingly, after checking
things manually, I just spotted that putty's plink is not coming as a
package with that name but that it is wrapped up to the package
putty-tools. This is just fine to me. I'll add a "Conflicts:
putty-tools" to the plink control file, upload plink's new version 1.04
and we are set.

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. 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.

Best,

Steffen