unrelated software install triggering an error from R's install script on Mac OS X 10.5

Simon Urbanek wrote:

On Dec 1, 2008, at 6:11 AM, Laurent Gautier wrote:

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.

... if you really want those files to prepend your PATH. You get  
what you deserve ;) I this case you don't want that and this is  
true for all unix platforms.

The point seems to be slightly missed here: the result of installing  
R is that there is no R executable in the path,

and that adding the only bin/ directory coming with the install to  
be path results in a broken system.

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.

Then you seem to be very unfamiliar with the unix way as it  
appears...

Ah ! the flourishing pronouncements on the R-lists...

I am surprised by this cherry pick one executable in bin/ / don't  
touch the PATH.

You are apparently unaware of the way R is setup ... Note that on  
most unix systems this is exactly what you get - the R_HOME/bin  
directory is tucked away in /usr/local/lib/R/bin which is never on  
your PATH since R installs the user-visible scripts to /usr/local/ 
bin. The same happens here.

I guess that we this comparing apples with oranges here:
a default R install is leaving binaries in the path when performing  
a default install, which does not seem to be the case here  
(therefore forcing a hunt for the executable for the R console and  
resulting in the present thread).

The point here is that there is no user-exposed bin/ directory (or  
copying of the "right" executables by default to a place commonly  
agreed by some UNIX audiences as proper for binaries), and that the  
only bin/ found contains executables one should not get in his/her  
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.

Mac OS X is case-sensitive. Case-sensitivity is an option of the  
mounted file system and you can choose either. It is common to use  
case-insensitive fs for historical reasons (compatibility with  
older software), but you don't have to.

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.

If you want to override the system ones, yes. But you better know  
what you're doing ;).

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).

.. which leads to quite a few problems on its own. That's why  
you're entirely on your own if you do so (and likely to run into  
problems where Fink replaces systems parts with non-standard  
binaries).

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

You overlooked quite a bit of documentation of unix and R - pretty  
much none of it is OS X - specific.
Cheers,
S