[R] Does R ever stop responding without a message?

MacQueen, Don macqueen1 at llnl.gov
Mon Jul 15 18:34:25 CEST 2013

It is a (very) large marked point process object that is being split (see
original post), and that is some other kind of structure. So I think all
bets are off, in terms of what kind of duration to expect.

The folks on r-sig-geo might be able to help with suggestions for faster

In terms of monitoring the process, I have a couple of suggestions.

The first is to turn on profiling (see ?Rprof). Unless things changed in R
3.x.x, Rprof writes to a file as it profiles, and one could watch the file
grow to determine that processing is still taking place. Admittedly, it's
a cheap trick, and runs the risk of slowing the process, especially if the
profile file gets big.

The other is to do the split manually with a loop. This way, one could
insert cat() statements to track the progress. This is probably what I
would do first. Indeed, one could also write timestamps and track the rate
at which splitting is taking place (i.e., is it getting slower and slower).


Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550

On 7/15/13 2:50 AM, "Jim Holtman" <jholtman at gmail.com> wrote:

>a 'split' function should not take hours to complete.  I will not even
>wait a couple of minutes for one until I look at other approaches.  Can
>you at least show what the command looks like and what the structure of
>the data is.  Are you trying to split a dataframe on multiple criteria?
>I tend to use 'data.table' for some of these operation, or split the
>indices of a dataframe instead of the data.  My own criteria is that if a
>single base function call is taking more than a minute, I see if there
>are options.
>This is also a case of "tell me what you want to do, not how you want to
>do it".
>Sent from my iPad
>On Jul 14, 2013, at 23:24, L S <losedaghat at gmail.com> wrote:
>> Thanks Jim and David for your helpful feedback.  I still have not
>>terminated RStudio (and it still has not gone to completion).  A few
>>observations I forgot to mention is that the red "stop" icon is showing
>>in RStudio so I am unable to enter any new commands.  Also there is a
>>blinking cursor under the "> command" I ran with no > before the cursor.
>> David--Looking at the activity monitor, RStudio is using anywhere from
>>0.4-1% of CPU while another process called rsession is using anywhere
>>from 17-23% CPU.  Does this mean it has given up processing the R
>>command?  If so, is there anything I can do to ensure this won't happen
>>next time I try to run the command with my data?
>> (Also, how can you tell if the process is using virtual memory?)
>> Jim--What I'm running now is just a single instruction using the split
>>function, so I would not be able to put in the progress messages.  But,
>>that's a great idea! I will keep that in mind if I run into problems
>>with scripts in the future.
>> Thank you.
>> On Sun, Jul 14, 2013 at 6:46 PM, jim holtman <jholtman at gmail.com> wrote:
>> If you are writing a script that you know will take a long time to
>>process, "pepper" it with "progress" reports so you know what part of
>>the script it is in and when it is going around loop.  On some of my
>>long scripts, I will print out a message every n'th time through the
>>loop so that I know if it making progress.  I position them so that I
>>get out a message every minute or so.  Also make sure the GUI is not
>>buffered, or better, follow each status with a 'flush.console()' to put
>>the message out to the screen.  This will give you a feeling of what
>>progress you are making.
>> On Sun, Jul 14, 2013 at 5:40 PM, L S <losedaghat at gmail.com> wrote:
>> Hi,
>> Have any of you ever encountered a situation where R stops processing an
>> instruction but does not give a "not responding" message?
>> The reason I ask is I am working in RStudio (Mac OS/X 10.7, 1.8 Ghz i7,
>> GB DDR3) and the instruction I entered in the command line pane is still
>> being processed since last night around 7 PM.  I expected it to take on
>> order of 8-12 hours to complete, but I'm nearing 24 hours with no
>> no messages, etc.
>> The command is essentially splitting the a ppp (marked point pattern)
>> a tessellation/grid.  There are about a couple million points in the
>> pattern and each has a vector of four marks.  That said, I processed a
>> similar command with 700,000 points in the pattern (each point with a
>> vector of two marks) yesterday and it took only around 3 hours.
>> Is there anyway I can be certain the command is being processed?  I
>> want to abort prematurely if I know it will go to completion.  How long
>> would you give it before you knew for certain it would not complete?
>> Any guidance you could offer would be much appreciated.
>> Thanks,
>> Lily
>>         [[alternative HTML version deleted]]
>> ______________________________________________
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>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
>> -- 
>> Jim Holtman
>> Data Munger Guru
>> What is the problem that you are trying to solve?
>> Tell me what you want to do, not how you want to do it.
>	[[alternative HTML version deleted]]
>R-help at r-project.org mailing list
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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