[BioC] Installing Biocondutor under Debian r

[A.J. Rossini]

>>>>> "johannes" == Johannes Husig <derwisch@panix.com> writes:

    johannes> Cheers,
    johannes> after installing Bioconductor on my Debian system I was
    johannes> surprised to see that the new files were installed in
    johannes> the /usr/lib/R tree. 

    johannes> Under Debian, this is considered offensive behaviour.
    johannes> Debian assumes that the /usr tree (save /usr/local) is
    johannes> only touched by the distribution, and that non-distributional
    johannes> packages are to be installed in the /usr/local tree. 

    johannes> So people who use Debian and related distributions should
    johannes> be advised to change the paths according to their system.

    johannes> Many things run automatically under Bioconductor so sometimes
    johannes> users are tempted to perform things that are not in line with
    johannes> the philosophy of the underlying system.


This is actually true of ANY R INSTALL under the Debian system, unless
you specify a local install.  Doesn't matter if it's Bioconductor or
not!  It is a well known problem to the Debian maintainer, and
discussion as to the "right" solution is still on going...
 
Sounds like you installed under root, eh?  (or via sudo).  Else, you'd
get an error.

I've got Debian packages for Bioconductor (takes care of some of the
associated requirements, such as PostgreSQL for AnnBuilder, etc).
I'll make the archive available as soon as they get vetted by a
developer I've been working with (the debian R maintainer)....

best,
-tony

-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini@u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini@scharp.org
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