R help - Aug 2005 - Advice about system for installing & updating all R package in a Linux Lab?

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

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?
> 
>

On 08/19/05 16:23, 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)
I used to do this:

    update.packages()
    cp <- CRAN.packages()[,1]
    ip <- installed.packages()[,1,]
    install.packages(setdiff(cp,ip))

But now it looks like you can do this:

    install.packages(new.packages())

Jon
-- 
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron

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 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

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.
  One other option is if those packages get in Fedora Extras. :-)
  I intend to submit some packages to FE, and then upgrading will be a lot
easier.

  What are the packages that interest you?

-- 
Jos伱仼 Ab伱伃lio