[BioC] Getting LimmaGUI to run

chris umbricht cumbrich at jhmi.edu
Fri Jul 15 18:37:58 CEST 2005

>> Stefano,
>> re: "if R quits "unexpectedly" the finder will tell you, just press 
>> the button concerning the crash report"
>> R quits immediately after starting up, and the finder does not 
>> generate a crash report.
> umh, probably the report is generated but not shown by the Finder.

Well, I do get finder reports if other  Apps crash... if you are right, 
can I retrieve it somewhere?

>> As I understood from both your and Rob's comments, it appears simply 
>> that my .RData file contains X11 dependent processes, eg tkltk.
>> So I can avoid the problem by prestarting the X11 window, which is 
>> fine.
>> My question to you is, how do I undo that dependecy in the R.app 
>> (1.12, build 1622) short of trashing the RData file from within the 
>> terminal window?
> try the following with X11 running
> launch R.app (should not quit)
> and in R Console
> > (.packages())

 >  (.packages())
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     
"datasets"  "base"

However, this is how the R.app console comes up on its own:

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

Loading Tcl/Tk interface ... done
[Previously saved workspace restored]

It seems the culprit is the loading tcltk ... line.

How Do I change/remove it from the default start up?

> does tcltk appear in this list? If so type
> > detach(package:tcltk)
> and check that it is no longer there with
> > (.packages())
> now
> > save.image()
> quit R, shut down the X11 window server and try to restart R.app. Let 
> me know
> stefano
>> Am I wrong in assuming the workspace menu items are designed to get 
>> back to the original, non-X11 dependent environment? If so, is there 
>> another way?

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