[R] debug an error that incapacitates R?

[Rolf Turner]

Wouldn't sink.number() give you a handle on whether
the problem is that there is an invalid sink() in effect?

On 15/12/2009, at 10:55 AM, Brian Diggs wrote:

>> -----Original Message-----
>> From: Liviu Andronic [mailto:landronimirc at gmail.com]
>> Sent: Sunday, December 13, 2009 4:05 AM
>> To: Duncan Murdoch
>> Cc: r-help at r-project.org Help
>> Subject: Re: [R] debug an error that incapacitates R?
>>
>> Hello
>> And thank you for the quick answer.
>>
>> On 12/13/09, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
>>>  I think you need to go back to old-fashioned debugging methods.
>>> Identify
>>> the line the triggers the error, by using debug() and single  
>>> stepping
>>> through sosInit(), or by adding print() or cat() statements to it  
>>> (or
>>> setting tracepoints with trace()), and seeing how many succeed  
>>> before
>>> things
>>> go bad.
>>>
>> Experimenting with browser() and subsequently with the step-through
>> debug() I managed to identify the first line that triggers the
>> "invalid connection" error:
>> doItAndPrint(paste("## Launching RSiteSearch, please be patient.."))
>
> I have seen this "invalid connection" type error when there is a  
> sink()
> active that does not have a valid connection associated with it.   
> In that
> case, any output generates the error.  Try issuing sink() commands  
> (without
> any arguments) to remove any active sinks.  When there are not any  
> more
> sinks you will get the message:
>
> Warning message:
> In sink() : no sink to remove
>
>>>  Once you see the bad line, it may be obvious what's wrong with it,
>>> or you
>>> may need to ask for help, by putting together a minimal example that
>>> triggers it.
>>>
>> Unfortunately, there is nothing obviously wrong with the call, nor
>> with the environment. Omitting the line makes the function work in  
>> all
>> my test cases. I will contact John Fox on this.
>
> If it is an invalid sink, this would just be the first call that  
> generates
> output.  It would be a sink somewhere before that that is setting  
> up a bad
> connection (which doesn't cause problems until something is to be  
> written).
>
>> Thank you
>> Liviu
>>
>
> --
> Brian Diggs, Ph.D.
> Senior Research Associate, Department of Surgery, Oregon Health &  
> Science University
>
>
>
>
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> and provide commented, minimal, self-contained, reproducible code.


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