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

[Henrik Bengtsson]

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}
   fi
fi

Cheers

Henrik

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
> 
> http://support.stat.ucla.edu/view.php?supportid=30
> 
> 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 = "http://lib.stat.cmu.edu/R/CRAN/")
> update.packages(ask=F)
> x <- packageStatus(repositories="http://cran.r-project.org/src/contrib")
> 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):
> 
> http://lark.cc.ku.edu/~pauljohn/software/R/R_installAll.Rout
> 
> 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?
> 
>