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

[Paul Johnson]

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?


-- 
Paul E. Johnson                       email: pauljohn at ku.edu
Dept. of Political Science            http://lark.cc.ku.edu/~pauljohn
1541 Lilac Lane, Rm 504
University of Kansas                  Office: (785) 864-9086
Lawrence, Kansas 66044-3177           FAX: (785) 864-5700