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

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat 20 Aug 2005 - 15:28:23 EST

This is based on the pre-2.1.0 ideas. Try

update.packages(ask=FALSE)
install.packages(new.packages(), dependencies=TRUE)

However, I would suggest that you set up each student with a library, say ~/R/library, and point R_LIBS at it (set in Renviron.site). That's what we do for Windows, and it seems successful. (We have other reasons to want very complete central Linux setups, one being that we run more than one archtecture where personal libraries are a little harder to manage.)

On Fri, 19 Aug 2005, 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

Many of the commands there are now or about to be deprecated. See my article in the current R-News.

> 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?

None at all. We do something similar (but based on new.packages and with a stoplist of packages that we know will not install).

-- 
Brian D. Ripley,                  ripley@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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Received on Sat Aug 20 15:33:21 2005

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