R SIG Debian - Nov 2005 - setting R_LIBS

Hello,

I'm adding a private library tree in my home directory by adding this to
my ~/.Renviron:

R_LIBS="~/R/library:${R_LIBS}"

so that once in R:

R> cat(Sys.getenv("R_LIBS"), "\n")
~/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library


Is this the best way to proceed?


Cheers,

-- 
Sebastian P. Luque

On 30 November 2005 at 16:44, Sebastian Luque wrote:
| I'm adding a private library tree in my home directory by adding this to
| my ~/.Renviron:
| 
| R_LIBS="~/R/library:${R_LIBS}"
| 
| so that once in R:
| 
| R> cat(Sys.getenv("R_LIBS"), "\n")
|
~/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
| 
| 
| Is this the best way to proceed?

Sure, after all it's in the FAQ (Q5.2) and documented under help(Startup).  

I also use it at work on different system where 

	a) I may or may not have write permissions (Linux), or 

	b) want to keep my package directory outside of the versioned R
	   directory tree (Windoze).

So thumbs up from me.  And under Debian, thanks to the useful expansion of
R_LIBS from pre-defined values, you get your own as well as the systems
directory in /usr/lib and /usr/local/lib.  

The only other thing to consider would be a multi-user setting. You could
experiement with Renviron.site if you want to leave the conffile
/etc/R/Renviron alone.  I have not tried this.

Dirk

-- 
Statistics: The (futile) attempt to offer certainty about uncertainty.
         -- Roger Koenker, 'Dictionary of Received Ideas of Statistics'

Hi again,

My new private library setting needs some further tweaking apparently.  Two
things seem to be wrong:

1) Although package compilation finishes without problems, I get this message at
   the end:

,-----
| Warning message:
| cannot create HTML package index in: tools:::unix.packages.html(.Library) 
`-----

2) when doing library("package"), I get this:

,-----
| Error in dyn.load(x, as.logical(local), as.logical(now)) : 
| 	unable to load shared library
'/home/sluque/R/library/chron/libs/chron.so':
|   /home/sluque/R/library/chron/libs/chron.so: failed to map segment from
shared object: Operation not permitted
| Error: package/namespace load failed for 'chron'
`-----

None of this happens when using the predefined library at
/usr/local/lib/R/site-library.  Perhaps I need to set some particular
permissions on this directory?


Thanks,

-- 
Sebastian P. Luque

Sebastian Luque <spluque at gmail.com> wrote:
> 1) Although package compilation finishes without problems, I get this
message
> at the end:
> ,-----
> | Warning message:
> | cannot create HTML package index in: tools:::unix.packages.html(.Library)
> `-----

To clarify what I mean here -- this is the last message after installing a
package in the new private library.  It occurs with any package I try to
install.


Cheers,

-- 
Sebastian P. Luque