[R-SIG-Mac] help() start page - how to set

[Simon Urbanek]

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?
>>>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/statet-user
>>
>> 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')
> Sys.getenv('R_SESSION_TMPDIR')
>                                               R_SESSION_TMPDIR
> "/var/folders/kL/kLbJmLNyEWa6w5gv6nb60U+++TI/-Tmp-//Rtmpp01O7b"
>
> R> help.start()
> 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')
>               R_SESSION_TMPDIR
> "/Users/stavros/tmp/RtmpS1zNun"
>
> 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  
> know.
>
>> 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  
>> created.
>
> 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')
> 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.

Cheers,
S


> I can't really spend much more time on this now, but I think the  
> problem is somewhere buried in there ...
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Medical College of Cornell University
>
> http://cbio.mskcc.org/~lianos
>
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