From lgautier at gmail.com  Sun Nov 30 23:11:46 2008
From: lgautier at gmail.com (Laurent Gautier)
Date: Sun, 30 Nov 2008 23:11:46 +0100
Subject: [Rd] unrelated software install triggering an error from R's
 install script on Mac OS X 10.5
In-Reply-To: <5EF06ADB-867B-4151-BBD2-E8293BE42745@uos.de>
References: <49315329.7050703@gmail.com>
	<5EF06ADB-867B-4151-BBD2-E8293BE42745@uos.de>
Message-ID: <49330FA2.1030604@gmail.com>

Stefan Evert wrote:
> 
>> The steps needed to generate the error are:
>>
>> - install a binary distribution of R (default location)
>> - add R to the PATH
> 
> Did you actually add
> 
>     /Library/Frameworks/R.framework/Resources/bin/
> 
> to your PATH?  You're not supposed to do that!  What made you think so?

Coming from an UNIX background, adding a directory like bin/ to the PATH 
   does not appear unreasonable.

> This directory contains a range of support scripts for R which are not 
> intended for direct use from the command line or other programs.  In my 
> installation, there's just a symlink from /usr/bin/R to the R binary in 
> the directory above, which AFAIK is the only program you need to invoke 
> directly.

I am relatively new to OS X, so I cannot tell whether this is an R 
specificity, or the way things are usually done on OS X are somewhat 
very different from the UNIX way.
I am surprised by this cherry pick one executable in bin/ / don't touch 
the PATH.


> In your case, R's "INSTALL" script, which implements the "R CMD INSTALL" 
> functionality masks the standard "install" program in /usr/bin/install, 
> so Python's installer now picks up a completely wrong program.  Even if 
> you edit R's "INSTALL" script, it'll do something entirely different 
> from what you expect.

To my great dismay I am hearing here that Mac OS X is not case-sensitive.


> BTW, putting the R binary directory ahead of system directories such as 
> /usr/bin in your PATH is an even worse idea than including it there in 
> the first place. ;-)

I am used to the fact that adding a bin/ directory in the PATH (and 
*ahead* of all other components in the PATH) is the way to add custom 
binaries. I cannot exclude that I am missing some specificities of Mac 
OS X, but that idea seems to be at least shared by the fink project 
(their default install puts /sw/bin ahead of all the rest).


I suppose that there is a documentation for R-on-OS-X and that I 
overlooked it.



Laurent





> 
> 
> Best regards,
> Stefan Evert
> 
> [ stefan.evert at uos.de | http://purl.org/stefan.evert ]
> 
> 
>



[Rd] unrelated software install triggering an error from R's install script on Mac OS X 10.5
Laurent Gautier