R help - Apr 2005 - R_LIBS difficulty ?

Hi, R people.

I'm shy reporting this, as a bug in this area sounds very unlikely.  Did
I make my tests wrongly?  I'm still flaky at all this.  Let me dare
nevertheless, who knows, just in case...  Please don't kill me! :-)

Not so long ago, I wrote to this list:
> (For now, [the library code] works only for me when I do _not_ use `-l
> MY/OWN/LIBDIR' at `R CMD INSTALL' time, I surely made a simple
blunder
> somewhere.  Hopefully, I'll figure it out.)
Now using this line within `~/.Renviron':

   R_LIBS=/home/pinard/etc/R

my tiny package is correctly found by R.  However, R does not seem to
see any library within that directory if I rather use either of:

   R_LIBS=$HOME/etc/R
   R_LIBS="$HOME/etc/R"

The last writing (I mean, something similar) is suggested somewhere in
the R manuals (but I do not have the manual with me right now to give
the exact reference, I'm in another town).

Another hint that it could be expected to work is that the same
`~/.Renviron' once contained the line:

   R_BROWSER=$HOME/bin/links

which apparently worked as expected.  (This `links' script launches the
real program with `-g' appended whenever `DISPLAY' is defined.)

This is R 2.0.1, installed on SuSE 9.2.

-- 
Fran?ois Pinard   http://pinard.progiciels-bpi.ca

Fran?ois Pinard <pinard at iro.umontreal.ca> writes:
> Hi, R people.
> 
> I'm shy reporting this, as a bug in this area sounds very unlikely. 
Did
> I make my tests wrongly?  I'm still flaky at all this.  Let me dare
> nevertheless, who knows, just in case...  Please don't kill me! :-)
> 
> Not so long ago, I wrote to this list:
> 
> > (For now, [the library code] works only for me when I do _not_ use `-l
> > MY/OWN/LIBDIR' at `R CMD INSTALL' time, I surely made a simple
blunder
> > somewhere.  Hopefully, I'll figure it out.)
> 
> Now using this line within `~/.Renviron':
> 
>    R_LIBS=/home/pinard/etc/R
> 
> my tiny package is correctly found by R.  However, R does not seem to
> see any library within that directory if I rather use either of:
> 
>    R_LIBS=$HOME/etc/R
>    R_LIBS="$HOME/etc/R"
> 
> The last writing (I mean, something similar) is suggested somewhere in
> the R manuals (but I do not have the manual with me right now to give
> the exact reference, I'm in another town).
?Startup gets you there soon enough (and help.search(Renviron) points
you at Startup):

     Lines in a site or user environment file should be either comment
     lines starting with '#', or lines of the form 'name=value'.
The
     latter sets the environmental variable 'name' to 'value',
     overriding an existing value.  If 'value' is of the form
     '${foo-bar}', the value is that of the environmental variable
     'foo' if that exists and is set to a non-empty value, otherwise
     'bar'.  This construction can be nested, so 'bar' can be of
the
     same form (as in '${foo-${bar-blah}}').

so R_LIBS=${HOME}/etc/R is what should work. Notice that this is
processed by R internally, not by the shell, so syntax may differ from
the command-line equivalent.


-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907

On Sun, 10 Apr 2005, Fran?ois Pinard wrote:
> Hi, R people.
>
> I'm shy reporting this, as a bug in this area sounds very unlikely. 
Did
> I make my tests wrongly?  I'm still flaky at all this.  Let me dare
> nevertheless, who knows, just in case...  Please don't kill me! :-)
>
> Not so long ago, I wrote to this list:
>
>> (For now, [the library code] works only for me when I do _not_ use `-l
>> MY/OWN/LIBDIR' at `R CMD INSTALL' time, I surely made a simple
blunder
>> somewhere.  Hopefully, I'll figure it out.)
>
> Now using this line within `~/.Renviron':
>
>   R_LIBS=/home/pinard/etc/R
>
> my tiny package is correctly found by R.  However, R does not seem to
> see any library within that directory if I rather use either of:
>
>   R_LIBS=$HOME/etc/R
>   R_LIBS="$HOME/etc/R"
Correct, and as documented.

See the description in ?Startup, which says things like ${foo-bar} are 
allowed but not $HOME, and not ${HOME}/bah or even ${HOME}.

But R_LIBS=~/etc/R will work in .Renviron since ~ is intepreted by R in 
paths.
> The last writing (I mean, something similar) is suggested somewhere in
> the R manuals (but I do not have the manual with me right now to give
> the exact reference, I'm in another town).
It is not mentioned in an R manual, but it is mentioned in the FAQ.
R_LIBS=$HOME/etc/R will work in a shell (and R_LIBS=~/etc/R may not).
> Another hint that it could be expected to work is that the same
> `~/.Renviron' once contained the line:
>
>   R_BROWSER=$HOME/bin/links
>
> which apparently worked as expected.  (This `links' script launches the
> real program with `-g' appended whenever `DISPLAY' is defined.)
Yes, but that was not interpreted by R, rather a shell script called by R.

-- 
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