[R] Upgrade 'R'

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Sep 2 14:03:45 CEST 2008

On Tue, 2 Sep 2008, Keith Jewell wrote:

> "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote in message
> news:alpine.LFD.1.10.0809021124300.12240 at gannet.stats.ox.ac.uk...
>> On Tue, 2 Sep 2008, Keith Jewell wrote:
>>> As possible help to others, and also as a request for comments on how I
>>> might do things better, I describe how I've recently altered my system to
>>> handle this.
>>> I'm on a Windows Server 2003 network and the R installation is accessible
>>> to
>>> many others. Everyone has "read" access to all installation files, but
>>> only
>>> I have write access. I do _not_ have Administrator privileges on the
>>> server,
>>> so I cannot make/change registry entries.
>>> R versions are in an R folder tree, which also holds the version
>>> independent
>>> library folder.
>>> //Server02/stats/R
>>> //Server02/stats/R/R-2.7.0
>>> //Server02/stats/R/R-2.7.1
>>> //Server02/stats/R/R-2.7.1pat
>>> //Server02/stats/R/R-2.7.2
>>>   :
>>> //Server02/stats/R/library
>>> In each version I have edited /etc/Rprofile.site to include the line
>>> .libPaths("//Server02/stats/R/library")
>>> The "default" libraries (base, boot, class...) are installed into the
>>> relevant version specific .../R-n.n.n/library/ folder by the windows
>>> installer program (e.g. R-2.7.2-win32.exe).
>>> Occasionaly, and after installing a new R-version,  I update all the
>>> downloaded libraries in the version independent
>>> //Server02/stats/R/library/
>>> folder with a simple update.packages().
>>> HTH. Comments welcome.
>> Please read the rw-FAQ for more details and insight, especially in using
>> Renviron.site (here you want to set R_LIBS_SITE: see ?libPaths) and using
>> update.packages(checkBuilt=TRUE, ask=FALSE)
>> For example, my sysadmins have Windows R installed locally (via the MSI
>> installer), and then have on each machine in etc/Renviron.site have
>> R_LIBS_SITE=N:/R/library/2.7
>> R_LIBS_USER=P:/R/win-library/2.7
>> This allows both common packages and user-specific packages to be stored
>> on SMB-mounted drives.  (N: is common to all machines, P: is 'personal' --
>> we use mapped drives rather than shares to allow quick changes of server)
>> There are two reasons we install locally.  The first is performance: if 20
>> machines in a lab start R up simultaneously the network load is high.  The
>> second is that our security settings (and I believe the defaults these
>> days) disallow use of CHM help on network drives -- we remove the chtml
>> directories from packages installed on R_LIBS_SITE, so R defaults to text
>> help for those packages.
> Thanks Professor Ripley. I'd looked at the R Windows FAQ but  not carefully
> enough.Using Renviron.site does seem much more elegant than Rprofile.site.
> I've now included a line in Renviron.site
> R_LIBS_SITE=//Server02/stats/R/library
> I also note your use of site and personal libraries specific to "first
> decimal"
> versions of R. Would you recommend others to follow this practice?

Yes: that is the level of compatibility.  (It is done automatically for 
personal libraries created by R: we set R_LIBS_USER because HOME is 
set incorrectly on some of our systems.)

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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