[BioC] Getting LimmaGUI to run

chris umbricht cumbrich at jhmi.edu
Fri Jul 15 17:47:15 CEST 2005


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.

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 

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?



On Jul 15, 2005, at 5:44 AM, stefano iacus wrote:

> On 11/lug/05, at 22:26, chris umbricht wrote:
>> Rob,
>> thanks for your feedback, and I do understand your directions, i.e. I
>> think I will be able to navigate this X11 dependency with your
>> suggestions.
>> I was trying to give Stefano some feedback, since he is heavily
>> involved in developing the OS X version of R.App, and I'm trying to
>> distinguish between my misunderstanding some elements of the GUI vs
>> having a corrupted installation. It seems to me that having to delete
>> the .RData file from the terminal should not be necessary as routine
>> measure...
>> I'm hoping he will chime in, since he asked me for more details
>> earlier, but I'm not sure what he needs.
> it R quits "unexpectedly" the finder will tell you, just press the 
> button concerning the crash report (I think is something like "send 
> report")
> stefano
>> On Jul 11, 2005, at 4:18 PM, Rob J Goedman wrote:
>>> Chris,
>>> Remove .RData (as in previous emails).
>>> Start R and close R. When it asks if you want to save
>>> the session, choose Save to create a new .RData file.
>>> I nearly always select Don't Save, which will not create a new
>>> .Rdata file.
>>> If you don't load tcltk, jpeg and/or png, e.g. used in marray, (maybe
>>> there are a few other packages that will require X11), you don't need
>>> X11 and it will not end up as a dependency in .RData.
>>> Or you can automatically start X11 when you login (Drag it to Login
>>> items of your Account is System Preferences).
>>> Rob
>>> On Jul 11, 2005, at 12:44 PM, chris umbricht wrote:
>>>> Right, so how do I change the .RData back to not containing tcltk
>>>> calls?
>>>> I tried the (to me) obvious steps of unchecking anything 
>>>> tcltk-related
>>>> in the manager, and trying to clear the workspace etc. without
>>>> apparent
>>>> effect...
>>>> c.
>>>> On Jul 11, 2005, at 12:39 PM, stefano iacus wrote:
>>>>> Hi Chris,
>>>>> no it has always been the case. And the problem is that probably 
>>>>> your
>>>>> .RData contains calls to tcltk.
>>>>> Any call to tcltk, X11 etc requires a X11 server to be running.
>>>>> btw, I need more detailed bug report that this.
>>>>> stefano

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