[R-SIG-Mac] help() start page - how to set
simon.urbanek at r-project.org
Tue Nov 18 15:22:06 CET 2008
On Nov 17, 2008, at 22:48 , Steve Lianoglou wrote:
> On Nov 17, 2008, at 9:04 PM, Bill Northcott wrote:
>> On 18/11/2008, at 12:37 PM, Steve Lianoglou wrote:
>>> I'm curious to see if using StatET is useful, too ... as this is
>>> quite eclipse/plugin specific, perhaps you'd get better feedback
>>> from the StatET mailing list?
>> I started there but they have no clue about MacOS.
> Oh ... I didn't see any messages related to this in their archives,
> so I thought maybe you didn't find them, sorry.
>> I was looking for someone who might understand how this stuff
>> normally works on a Mac and hence I might be able to see what is
>> going wrong.
> When you create a run config for R (Run > Run Confgurations ...), in
> the "Main" tab, you have a drop down box with "Launch" options. The
> Rterm option works, the RMI/JRI option doesn't.
> Ideally I guess we want RMI/JRI ... here's what happens.
> Launch R w/ Rterm
> I added --no-save in the Options/Arguments box, but I'm not sure
> that matters, anyway, when you run the config, this works:
> R> > Sys.getenv('R_SESSION_TMPDIR')
> R> help.start()
> Making links in per-session dir ... done
> If '/usr/bin/open' is already running, it is *not* restarted, and you
> must switch to its window.
> Otherwise, be patient ...
> # Browser pops up with the page you want
> Launch R w/ RMI/JRI
> Yes: bizarre. I can't get anything to work.
> I can effectively get the R_SESSION_TMPDIR to be "what I want" by
> setting the TMPDIR environment variable in the Run config's
> Environment tab. For instance, I have TMPDIR set to "/Users/stavros/
> tmp". The R_SESSION_TMPDIR var is then:
> R> Sys.getenv('R_SESSION_TMPDIR')
> I'm still getting some the same errors, though, as the R process
> isn't making the required directories. I wonder if it has something
> to do w/ java communicating the R process via RMI ... I don't really
>> It is attempting to access this .R directory in the location
>> defined by $R_SESSION_TMPDIR. At what point might R be expected
>> to create that? When I run R in a Terminal these directories get
> So, after playing w/ this for a bit, I guess that:
> (1) The $R_SESSION_TMPDIR is just created by monkeying with the
> environments defined TMPDIR variable, which we can change in the Run
> config's settings (like above)
> (2) The "RtmpS1zNun" is created when R starts up
> (3) The .R directory is then created after help.start() is executed.
> I got (2) and (3) when running from the Terminal.
> You know: I think I've realized what's going on, and I'm not sure
> how to fix it. It looks as if the running R process doesn't have the
> appropriate R environment variables set. For instance, in the RMI/
> JRI mode, look:
> R> Sys.getenv('USER')
> Likewise, the "help-links.sh" (in "/Library/Frameworks/R.framework/
> Versions/2.8/Resources/share/sh") script that the help.start()
> function uses requires environment variables like "R_DOC_DIR",
> "USER_R_HOME", to be set. All of these are empty. I tried setting
> the "R_DOC_DIR" to the appropriate location in the Run config's
> environment tab, but that's still not enough.
Apparently the way Eclipse is starting R is wrong. The recommended way
is to use the R shell wrapper even with JRI -- usually "R CMD foo"
will do the trick where foo is the script that starts Java.
> I can't really spend much more time on this now, but I think the
> problem is somewhere buried in there ...
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Medical College of Cornell University
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
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