[R-SIG-Mac] some errors

[Kasper Daniel Hansen]

Hi

I have recently (some days ago) started working on a Mac, and have a few 
"problems" to report:

So far I have been running R.app under Tiger as well as using R from 
within Emacs

1) In the "Preferences/Startup" menu, there is a spelling mistake: the 
option "Add $HOME/R/Library" should be "Add $HOME/Library/R" (I guess).

2) I tried installing Bioconductor binaries using the package menu. I 
can easily install binaries from CRAN. When I pick "bioconductor 
(binaries)" I can retrieve a list of packages from the mirror I am 
using, but when I click on an individal package and choose "Install 
selected", nothing happens. The console output is below. It seems to 
simply retieve the package list and nothing else. The fact that this 
happens only when I do Bioconductor and not CRAN seems to indicate that 
it is a Mac issue? I have installed the packages through other means, 
this is simply a user-report.

3) Could it be that R does not read environment variables when started 
on the terminal. 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

How do people solve the last issue: that of adding the user-dependent 
library, when using ESS/terminal.

The questions might be a bit basic, but still...

Kasper
***** Bioconductor install


R is free software and comes with ABSOLUTELY NO 
WARRANTY. You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES'
Content type 'text/plain; charset=ISO-8859-1' length 11224 bytes
opened URL
==================================================
downloaded 10Kb

trying URL 'http://www.bioconductor.org/bin/macosx/2.1/PACKAGES'
Content type 'text/plain; charset=ISO-8859-1' length 11224 bytes
opened URL
==================================================
downloaded 10Kb


******* R_LIBS probelm

north-mesh-wlan-87:~ kdh$ echo $R_LIBS
/Users/kdh/Library/R/
north-mesh-wlan-87:~ kdh$ R

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0 Patched (2005-05-12), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/Library/Frameworks/R.framework/Resources/library"
>