Re: [R] Advice about system for installing & updating all R package in a Linux Lab?

From: Henrik Bengtsson <>
Date: Sat 20 Aug 2005 - 09:11:48 EST

You can also provide the users with the option to add/update their own packages locally via install- and update.packages(). Here's a piece of bash code that sets R_LIBS for to a OS specific directory in the users account. Add it to the system wide startup script.

if test "${R_LIBS}" = ""; then

   # Get the OS type in lower case
   ostype=`uname -s | tr '[A-Z]' '[a-z]'`    export R_LIBS=${HOME}/R/R_LIBS/${ostype}/library/    if ! test -d "${R_LIBS}"; then
     mkdir -p ${R_LIBS}



Paul Johnson wrote:
> Good day:
> I'm administering 6 linux systems (FC4) in a student lab and worry that
> users may want packages that are not installed. I get tired of adding
> them one by one. Then I happened upon this page
> about installing all R packages from CRAN. That did not run as it was,
> but after some fiddling I arrived at the following script, which does
> run and it builds many packages and reports failures on the rest:
> #R_installAll.R
> options(repos = "")
> update.packages(ask=F)
> x <- packageStatus(repositories="")
> st <- x$avai["Status"]
> install.packages(rownames(st)[which(st$Status=="not installed")],
> dependencies=T)
> If I run that in batch mode (as root, of course)
> > R CMD BATCH R_installAll.R
> It produces some informative output. Some packages don't build because
> they are for Windows. As Prof Ripley mentioned recently, some packages
> don't build because of gcc-4.0.1. Some fail because I don't have some
> requisite libraries installed. I try to deduce which FC packages may be
> used to fix that and iterate the process now and then.
> But, for the most part, the packages to be OK (as far as I can tell).
> The output of a recent update is posted on the net here, in case you are
> interested to see (this lists the ones that don't build plus the
> successful updates):
> I can't see how this does any damage, since the packages that don't
> build are very graceful about erasing themselves, and the ones that do
> build are automatically available for the users.
> Can you see any downside to scheduling this process to run as a cron
> job, say once per week, to keep packages up to date?
> mailing list PLEASE do read the posting guide! Received on Sat Aug 20 09:17:15 2005

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