R help - Mar 2010 - [R-SIG-Mac] How to interrupt an R process that hangs

+1--this is the single most-annoying issue with R that I know of.

My usual solution, after accomplishing nothing as R spins idly for a couple
hours, is to kill the process and lose any un-saved work.  save.history() is
my friend, but is a big delay when you work with big data sets as I do, so I
don't run it after every command.

I have cc'd r-help here, however, because I experience this problem with
non-OSX R as well...when I run it in Linux or from the OSX command-line (I
compile R for Darwin without aqua/R-framework), the same thing happens.

Is there some way around this? Is this a known problem?

Google searching suggests no solution, timeline, or anything, but the
problem has been annoying users for at least twelve years:
http://tolstoy.newcastle.edu.au/R/help/9704/0151.html

Cordially,
Adam

On Mon, 15 Mar 2010, Matthew Keller wrote:
> HI all,
>
> Apologies for this question. I'm sure it's been asked many times,
but
> despite 20 minutes of looking, I can't find the answer. I never use
> the GUI, I use emacs, but my postdoc does, so I don't know what to
> tell her about the following:
>
> Occasionally she'll mess up in her code and cause R to hang
> indefinitely (e.g., R is trying to do something that will take days).
> In these situations, is there an option other than killing R (and the
> work you've done on your script to that point)?
>
> Thank you,
>
> Matthew Keller
>
>
> -- 
> Matthew C Keller
> Asst. Professor of Psychology
> University of Colorado at Boulder
> www.matthewckeller.com
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

On 15/03/2010 2:42 PM, Adam D. I. Kramer wrote:
> +1--this is the single most-annoying issue with R that I know of.
>
> My usual solution, after accomplishing nothing as R spins idly for a couple
> hours, is to kill the process and lose any un-saved work.  save.history()
is
> my friend, but is a big delay when you work with big data sets as I do, so
I
> don't run it after every command.
>
> I have cc'd r-help here, however, because I experience this problem
with
> non-OSX R as well...when I run it in Linux or from the OSX command-line (I
> compile R for Darwin without aqua/R-framework), the same thing happens.
>
> Is there some way around this? Is this a known problem?
>
> Google searching suggests no solution, timeline, or anything, but the
> problem has been annoying users for at least twelve years:
> http://tolstoy.newcastle.edu.au/R/help/9704/0151.html
>   
In the Windows GUI, the Esc key sets a flag which will cause 
computations to cease the next time the flag is checked. Unix-like 
systems do the same thing through signals.  SIGINT should eventually 
stop the computation.  How you send one of those in the OSX gui I don't 
know, but it works on a Linux system to run the command

 kill -s INT <PID>

where <PID> is the R process ID.  (Ctrl-C also works in that situation, 
but I'm assuming it's not available to you.)

In either case, I think it's possible to still end up in an unending 
loop, if you're doing some computation that never returns to the R 
evaluator.  (This might not be true in Unix-like systems.  They'll 
probably process the signal faster than Windows will see the Esc key, 
but I don't think that causes an immediate break when external code
is running.)  The key is to write your external code to check for user 
interrupts every now and then.

Duncan Murdoch
> Cordially,
> Adam
>
> On Mon, 15 Mar 2010, Matthew Keller wrote:
>
> > HI all,
> >
> > Apologies for this question. I'm sure it's been asked many
times, but
> > despite 20 minutes of looking, I can't find the answer. I never
use
> > the GUI, I use emacs, but my postdoc does, so I don't know what to
> > tell her about the following:
> >
> > Occasionally she'll mess up in her code and cause R to hang
> > indefinitely (e.g., R is trying to do something that will take days).
> > In these situations, is there an option other than killing R (and the
> > work you've done on your script to that point)?
> >
> > Thank you,
> >
> > Matthew Keller
> >
> >
> > -- 
> > Matthew C Keller
> > Asst. Professor of Psychology
> > University of Colorado at Boulder
> > www.matthewckeller.com
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

On Mar 15, 2010, at 14:42 , Adam D. I. Kramer wrote:
> +1--this is the single most-annoying issue with R that I know of.
>
> My usual solution, after accomplishing nothing as R spins idly for a  
> couple
> hours, is to kill the process and lose any un-saved work.   
> save.history() is
> my friend, but is a big delay when you work with big data sets as I  
> do, so I
> don't run it after every command.
>
> I have cc'd r-help here, however, because I experience this problem  
> with
> non-OSX R as well...when I run it in Linux or from the OSX command- 
> line (I
> compile R for Darwin without aqua/R-framework), the same thing  
> happens.
>
> Is there some way around this? Is this a known problem?
>
"Hanging" for a long period of time is usually caused by poorly  
written C/Fortran code. You can always interrupt R as long as it is in  
the R code. Once you load a package that uses native code (C/ 
Fortran/..) you have to rely on the sanity of the developer to call  
R_CheckUserInterrupt() or rchkusr() often enough (see 6.12 in R-ext).  
If you have some particular package that does not do that, I would  
suggest alerting the author. By definition this requires cooperation  
from authors, because interrupting random code forcefully (as it was  
possible many years ago) creates leaks and unstable states.

Cheers,
Simon


> Google searching suggests no solution, timeline, or anything, but the
> problem has been annoying users for at least twelve years:
> http://tolstoy.newcastle.edu.au/R/help/9704/0151.html
>
> Cordially,
> Adam
>
> On Mon, 15 Mar 2010, Matthew Keller wrote:
>
>> HI all,
>>
>> Apologies for this question. I'm sure it's been asked many
times, but
>> despite 20 minutes of looking, I can't find the answer. I never use
>> the GUI, I use emacs, but my postdoc does, so I don't know what to
>> tell her about the following:
>>
>> Occasionally she'll mess up in her code and cause R to hang
>> indefinitely (e.g., R is trying to do something that will take days).
>> In these situations, is there an option other than killing R (and the
>> work you've done on your script to that point)?
>>
>> Thank you,
>>
>> Matthew Keller
>>
>>
>> -- 
>> Matthew C Keller
>> Asst. Professor of Psychology
>> University of Colorado at Boulder
>> www.matthewckeller.com
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>