[Rd] unrelated software install triggering an error from R's install script on Mac OS X 10.5
lgautier at gmail.com
Mon Dec 1 11:38:21 CET 2008
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
>>> 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
>>> 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
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
> 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.
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