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
/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,
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 ;).
Cheers,
S
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
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