[Rd] unrelated software install triggering an error from R's install script on Mac OS X 10.5
simon.urbanek at r-project.org
Tue Dec 2 07:31:07 CET 2008
On Dec 1, 2008, at 6:38 PM, Laurent Gautier wrote:
> 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,
Clearly a false statement, look in /usr/bin (both R and Rscript are
installed there) - hence there is no need for you to add anything ...
which is why I think this discussion is quite redundant ;).
> 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
> 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
>>>> 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-
>> 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
>>> 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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