[R] debug an error that incapacitates R?

[Brian Diggs]

> -----Original Message-----
> From: Rolf Turner [mailto:r.turner at auckland.ac.nz]
> Sent: Monday, December 14, 2009 2:07 PM
> To: Brian Diggs
> Cc: r-help at r-project.org Help
> Subject: Re: [R] debug an error that incapacitates R?
> 
> 
> Wouldn't sink.number() give you a handle on whether
> the problem is that there is an invalid sink() in effect?

It would.  I had forgotten about that function.

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
> >
> >
> >
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-
> > guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
> 
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