On 27/03/2010 4:48 PM, Seth Falcon wrote:
On 3/27/10 1:43 PM, Duncan Murdoch wrote:
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().
I'm confused. AFAICT, R_LIBS_USER _is_ put first. Following the advice
in the Admin manual, I created a directory matching the default value of
R_LIBS_USER (Sys.getenv("R_LIBS_USER") to see it). Then when I start R,
I get:
.libPaths()
[1] "/home/sfalcon/R/x86_64-unknown-linux-gnu-library/2.11"
[2] "/home/sfalcon/build/rd/library"
Isn't that what you want?
I didn't try it, I just read the documentation (in ?.libPaths). As I
read it it says the order is
R_LIBS, R_LIBS_USER, .Library.site, .Library
and some of those components can be missing.
So another way to put the user libs first is to specify the site libs in
.Library.site rather than in the environment variable.
Duncan Murdoch
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