From andreas.fischlin at env.ethz.ch  Sun Feb  1 22:29:48 2009
From: andreas.fischlin at env.ethz.ch (Andreas Fischlin)
Date: Sun, 01 Feb 2009 22:29:48 +0100
Subject: [Rd] R.home() of R 2.8.1 Mac OS X is wrong (PR#13494)
In-Reply-To: <alpine.LFD.2.00.0902011932050.30737@gannet.stats.ox.ac.uk>
References: <20090201185014.59DBD282EF48@mail.pubhealth.ku.dk>
	<alpine.LFD.2.00.0902011932050.30737@gannet.stats.ox.ac.uk>
Message-ID: <4986144C.8020108@env.ethz.ch>

Thank you all for the replies. However, I figured it now out, there is 
nothing broken. The reason I got confused is only because there are 
symbolic links used extensively and some tests failed in my script as a 
consequence (see below).

My installation is fine and looks in fact like this:

afischli$ cd /Library/Frameworks/R.framework
afischli$ ls -l
total 40
lrwxr-xr-x  1 root  admin   24 Jan 13 15:24 Headers -> 
Versions/Current/Headers
lrwxr-xr-x  1 root  admin   30 Jan 13 15:24 Libraries -> 
Versions/Current/Resources/lib
lrwxr-xr-x  1 root  admin   31 Jan 13 15:24 PrivateHeaders -> 
Versions/Current/PrivateHeaders
lrwxr-xr-x  1 root  admin   18 Jan 13 15:24 R -> Versions/Current/R
lrwxr-xr-x  1 root  admin   26 Jan 13 15:24 Resources -> 
Versions/Current/Resources
drwxrwxr-x  7 root  admin  238 Feb  1 20:17 Versions
afischli$ cd Versions
afischli$ ls -l
total 8
drwxrwxr-x  6 root  admin  204 May 24  2007 2.5
drwxrwxr-x  6 root  admin  204 Nov 30  2007 2.6
drwxrwxr-x  6 root  admin  204 Jan 13 15:24 2.8
lrwxr-xr-x  1 root  admin    3 Jan 13 15:24 Current -> 2.8

This means there is nothing broken. The consequence is that R commands 
such as:

 > R.home()
[1] "/Library/Frameworks/R.framework/Resources"
 > setwd(R.home())
 > getwd()
[1] "/Library/Frameworks/R.framework/Versions/2.8/Resources"

give differing answers, which means that a test such as

setwd(R.home())
if (getwd() == R.home()) {

always fails, although the setwd command was actually successful. Guess 
this all explains the problem and sorry for the bandwidth waste ;-)

Regards,
Andreas Fischlin

________________________________________________________________________
ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fischlin at env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax

             Make it as simple as possible, but distrust it!
________________________________________________________________________



Prof Brian Ripley wrote:
> It is present on my system (R reinstalled yesterday), so it looks like 
> you broke yours.
>
> More precisely, there is a link at 
> /Library/Frameworks/R.framework/Resources to the correct place.
>
> How did you think R could possibly work with this broken?  R.home() is 
> used all over the place in R's own scripts.
>
> On Sun, 1 Feb 2009, andreas.fischlin at env.ethz.ch wrote:
>
>> Full_Name: Andreas Fischlin
>> Version: 2.8.1
>> OS: Mac OS X 10.5.6
>> Submission from: (NULL) (84.75.178.229)
>>
>>
>> R.home() returns "/Library/Frameworks/R.framework/Resources" although 
>> there is
>> no such directory present. Inspecting the actual directory structure 
>> of the R
>> installation indicates that the correct value R.home() should contain 
>> is:
>> '/Library/Frameworks/R.framework/Versions/2.8/Resources'
>>
>> Detected by af, ETH Zurich / 1.Feb.2009 using R 2.8.1 under Mac OS X 
>> 10.5.6
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
-- 

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[Rd] R.home() of R 2.8.1 Mac OS X is wrong (PR#13494)
Andreas Fischlin