From pauljohn32 at gmail.com  Thu Jul 19 18:13:12 2012
From: pauljohn32 at gmail.com (Paul Johnson)
Date: Thu, 19 Jul 2012 11:13:12 -0500
Subject: [Rd] Are R packages supposed to be "relocatable"? (avoiding
	BioConductor scripts...)
Message-ID: <CAErODj_84GbOi4hL5sx43aDkh6YAqrAndDETf2uT2zH=mgy=LQ@mail.gmail.com>

I've asked a question in the BioConductor list about package
management. My solution depends on your answer to the following
question.

Are installed R packages "relocatable"?

I mean relocatable in the same sense that files in a RedHat RPM file
might be "relocatable" after compiling
(http://www.rpm.org/max-rpm/ch-rpm-reloc.html).  This allows one to
build a package as the ordinary user and then the root user can take
the result and put it wherever it fits well in the path (say,
/usr/local/lib/R/library).

Here is why I asked.  I manage packages in our cluster and some users
have asked me to install some BioConductor packages.  BioConductor
install documents expect me to run a script as root that does a bunch
of changes, and I'm just unwilling to do that.  If I have to do
something as root, it has to be something more focused like running a
particular R command (install.packages(), for example).  It seems
insane to me that they expect (http://www.bioconductor.org/install) a
root user to run

source("http://bioconductor.org/biocLite.R")
biocLite("limma")

If I could do the installs as me with their script, and then copy the
install folder into the system, then it would be OK, if the packages
would work.

Or perhaps post-processing is required to fiddle some paths inside
package files?

pj
-- 
Paul E. Johnson
Professor, Political Science    Assoc. Director
1541 Lilac Lane, Room 504     Center for Research Methods
University of Kansas               University of Kansas
http://pj.freefaculty.org            http://quant.ku.edu



[Rd] Are R packages supposed to be "relocatable"? (avoiding BioConductor scripts...)
Paul Johnson