R devel - Jun 2005 - motivation for setRepositories and chooseCRANmirror

I have some questions and observations about these:

Will these replace manually setting options(CRAN), which doesn't work in 
R-2.1.0?

In R-2.1.0, setRepositories() looks to see if options("repos")
contains
a CRAN entry and will not override that CRAN entry even if the 
$R_HOME/etc/repositories file (which setRepositories reads from) 
contains a  CRAN entry.  Why is this? The user could easily set 
options("repos") without the help of this function anyway? And 
chooseCRANmirror() obviously sets the CRAN entry correctly.

I've checked the latest nightly tarball, R-devel_2005-06-15.tar.gz, and 
this observations persists.

I also observe that the R-2.1.0 Rprofile in the base package sets 
options(repos=c(CRAN="@CRAN@")), so it seems that the only way to set 
the CRAN repository entry is either with chooseCRANmirror() or manually 
setting options("repos") or options("CRAN"). If this was not
the case,
then setRepositories() would choose the CRAN entry from 
$R_HOME/etc/repositories.

In R-2.1.0 and in R-devel_2005-06-15.tar.gz, the R-admin manual suggests 
that for packages to be downloaded and installed within R should set 
options(CRAN = "http://cran.us.r-project.org/"). Will this be changed
to
calling chooseCRANmirror()?

 From an administrator's point of view, I would like to have the CRAN 
option set automatically on R startup for ALL users. That way I don't 
have to set this option before calling update.packages().


-- 
Jeffrey Horner       Computer Systems Analyst         School of Medicine
615-322-8606         Department of Biostatistics   Vanderbilt University

Jeffrey Horner wrote:
> I have some questions and observations about these:
> 
> Will these replace manually setting options(CRAN), which doesn't work
in
> R-2.1.0?
> 
> In R-2.1.0, setRepositories() looks to see if options("repos")
contains
> a CRAN entry and will not override that CRAN entry even if the 
> $R_HOME/etc/repositories file (which setRepositories reads from) 
> contains a  CRAN entry.  Why is this? The user could easily set 
> options("repos") without the help of this function anyway? And 
> chooseCRANmirror() obviously sets the CRAN entry correctly.
> 
> I've checked the latest nightly tarball, R-devel_2005-06-15.tar.gz, and
> this observations persists.
> 
> I also observe that the R-2.1.0 Rprofile in the base package sets 
> options(repos=c(CRAN="@CRAN@")), so it seems that the only way to
set
> the CRAN repository entry is either with chooseCRANmirror() or manually 
> setting options("repos") or options("CRAN"). If this
was not the case,
> then setRepositories() would choose the CRAN entry from 
> $R_HOME/etc/repositories.
> 
> In R-2.1.0 and in R-devel_2005-06-15.tar.gz, the R-admin manual suggests 
> that for packages to be downloaded and installed within R should set 
> options(CRAN = "http://cran.us.r-project.org/"). Will this be
changed to
> calling chooseCRANmirror()?
> 
>  From an administrator's point of view, I would like to have the CRAN 
> option set automatically on R startup for ALL users. That way I don't 
> have to set this option before calling update.packages().
> 
> 

Hence, I have in our department's R installation's 
.../R/etc/Rprofile.site file (which is intended for configurations that 
apply to all users):

options(repos = c(
           CRAN = "http://umfragen.sowi.uni-mainz.de/CRAN",
           CRANextra = "http://www.stats.ox.ac.uk/pub/RWin"))


Uwe Ligges