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Again: Bug#503367: plink: file conflict with putty-tools


in October last year there was a longish discussion about name space
pollution regarding plink.  If you like to spend some time you should
read the complete log of #503367 [1].

I decided to put an end now on this issue to make sure it will
not remain as is for ever and renamed the entry in /usr/bin.
This is explained in README.Debian of this package (see svn[2]).

Two questions are left on my side:

  1. On the one hand plink upstream claimed on their website[3] that
     Debian *has* renamed plink to snplink (which is not really true
     because the discussion ended without any real action).  But Gentoo
     went the same road to "follow" Debian.

     So there is one established way which is accepted upstream to handle
     this problem.

     On the other hand there is this other biological project which
     has a snplink as well.[4]  While chances are not really high
     that this software will also be packaged - you can not know.

     So what is better: Just seeking for another name which hopefully
     is singular and asking upstream as well as Gentoo to change as
     well or live with the small risk to run the same circle of name
     space pollution in case the other snplink will be packaged?

  2. Is the information that plink was renamed to snplink visible
     enough or should I rather use a debconf note to make users really
     aware what they have to do?

Kind regards


[1] http://bugs.debian.org/503367
[2] http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/debian/README.Debian?op=file&rev=0&sc=0
[3] http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
[4] http://www.icr.ac.uk/research/research_sections/cancer_genetics/cancer_genetics_teams/molecular_and_population_genetics/software_and_databases/index.shtml


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