some errors

Thanks for all the help.

First a summary: amongst the very many help suggestion, the best 
approach seems to be to use ~/.Renviron: in that file it is possible to 
set "environment" variables which are used even if there is no 
environment, such as when start the R GUI. This means that the values 
will be used in every invocation fo R - under shell, in Carbon Emacs, in 
the GUI.

Now, I actually tried that out without success before my post. I have 
done some further research and I think I have found some kind of bug 
(or else something very strange).

First off: I have tried everything on a Linux system running R-2.0.1 
where it works as expected.

My .Renviron is as follows 
 R_LIBS=/Users/kdh/Library/R/library
 R_PAPERSIZE=letter
 R_EDITOR=/usr/bin/nano
It is being parsed begause the settings affect the papersize and the 
editor used by R. The problem is the R_LIBS, and it is quite strange. 
Now, I have removed everything from my .profile as seen by

grue:~ kdh$ echo $R_LIBS

grue:~ kdh$ R

R : Copyright 2005, The R Foundation for Statistical Computing
<SNIP: R elcome message>

.libPaths()

[1] "/Library/Frameworks/R.framework/Resources/library"

Sys.getenv("R_LIBS")

R_LIBS 
"/Users/kdh/Library/R/library"

.libPaths(Sys.getenv("R_LIBS"))
.libPaths()

[1] "/Users/kdh/Library/R/library"                     
[2] "/Library/Frameworks/R.framework/Resources/library"

What is appearent from the transcript is
1) R_LIBS is actually set as seen by Sys.getenv.
2) This does not affect .libPaths()
3) However, passing R_LIBS to .libPaths() sets up everything correctly.

This baffles me quite a lot... I think it most be a mac bug since it 
works under Linux (ok, on an older version, but still...)

Just for completeness sake: I am running Tiger, with the R-2.1.0 patched 
version. I do not have administration privileges, but it seems to me 
that the permissions on ~/Library/ and subdirectories are as they ought 
to be. R is owned by root.

And finally, I realized that the typo in preferences probably should be 
corrected to $HOME/Library/R/library (although I must add that this 
setting is also not reflected in .libPaths())

Kasper

Or you can just

(setenv "R_LIBS" (format "%s/Library/R/library" (getenv "HOME")))

in your .emacs. You can also set your DISPLAY variable there as well.  
I'm sure if you were VERY enterprising you could write some elisp  
that would snarf your .profile, parse it and then run the elisp  
equivalents.

On Jun 8, 2005, at 8:48 PM, Seth Falcon wrote:

Hi Kasper,

On  8 Jun 2005, k.hansen@biostat.ku.dk wrote:

On the terminal as well as using ESS (Emacs) I can not get
.libPaths() to include /Users/kdh/Library/R despite the fact that I
have exported it from ~/.profile and the variable is set (output
below).  I have also tried using ~/.Renviron

I suspect the issue here is that Emacs isn't picking up your
environment.  GUI apps started from the Finder don't get the same
environment (.profile, .bash_profile, etc.) that apps started from the
Terminal do.

My solution: I start my Emacs from Terminal and then it inherits the
proper PATH and other env vars such as R_LIBS.

There is another possible solution that involves editing
~/.MacOSX/environment.plist, but I never managed to get that working
as I wanted.

Best,

+ seth

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

---
Byron Ellis (ellis@stat.harvard.edu)
"Oook" -- The Librarian

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen