[Rd] update.packages(1)

Duncan Murdoch murdoch at stats.uwo.ca
Sat Mar 27 21:43:09 CET 2010

On 25/03/2010 3:16 PM, Arni Magnusson wrote:
> I'm relaying a question from my institute's sysadmin:
> Would it be possible to modify update.packages() and related functions so 
> that 'lib.loc' accepts integer values to specify a library from the 
> .libPaths() vector?
> Many Linux users want to update all user packages (inside the R_LIBS_USER 
> directory, e.g. ~/r/library) and none of the system packages (inside the 
> /usr directory, e.g. /usr/lib64/R/library), because they don't have write 
> privileges to update the system packages.
> Currently, this can be done by pressing 'y RET' for all the user packages 
> and 'RET' for all the system packages. This hard work and careful reading 
> when there dozens of packages. Another way is to run
>    update.packages(Sys.getenv("R_LIBS_USER"))
> or:
>    update.packages(.libPaths()[1])

You could also save some work by putting ask=FALSE, or ask="graphics" in 
as another argument.  But isn't it easy enough to write your own 
function as a wrapper to update.packages, suiting your own local 
conventions?   It seems like a bad idea to make update.packages too 
friendly, when there are several different friendly front-ends for it 
already (e.g. the menu entries in Windows or MacOS GUIs).

> But it would be nicer for the user to type
>    update.packages(1)
> using a 'pos' like notation to indicate the first element of the 
> .libPaths() vector.
> ---
> A separate but related issue is that it would be nice if the R_LIBS_USER 
> library would be the first library by default. Currently, my sysadmin must 
> use Rprofile.site to shuffle the .libPaths() to make R_LIBS_USER first, 
> which seems like a sensible default when it comes to install.packages() 
> and remove.packages().
> This is R version 2.10.1 (2009-12-14) on x86_64-redhat-linux-gnu (Fedora 
> 11).

I didn't write it, but I suspect the current behaviour was intentional. 
  Without it, it would be hard to put the user library last, since 
.libPaths() adds things at the front.  Now you have a choice:  use the 
R_LIBS_USER environment variable to put it last, use a line in your 
Rprofile.site file to put something first.

Duncan Murdoch

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