R help - Jul 2005 - Way to make R idle for some time and try something again later

Hi, All;

I have a question. In R, what is the best way to make R idle for a while and
try something again later? For example, suppose there is an R job which
accesses a file that may be shared with other active jobs. So when the file
is being accessed by other job, your job will not be able to access the file
and your job will crash because of that. To avoid this, you want your job to
try to access the file repeatedly with some time interval, say every 10
seconds or something like that. Which is the best way to do this in R?

Thanks in advance,

Tae-Hoon Chung

Post-Doctoral Researcher
Translational Genomics Research Institute (TGen)
445 N. 5th Street (Suite 530)
Phoenix, AZ 85004
1-602-343-8724 (Direct)
1-480-323-9820 (Mobile)
1-602-343-8840 (Fax)

On 7/29/2005 3:13 PM, Tae-Hoon Chung wrote:
> Hi, All;
> 
> I have a question. In R, what is the best way to make R idle for a while
and
> try something again later? For example, suppose there is an R job which
> accesses a file that may be shared with other active jobs. So when the file
> is being accessed by other job, your job will not be able to access the
file
> and your job will crash because of that. To avoid this, you want your job
to
> try to access the file repeatedly with some time interval, say every 10
> seconds or something like that. Which is the best way to do this in R?
Sys.sleep(10) should give you a 10 second pause with very little impact 
on the system.

Duncan Murdoch

Which operating system are you using ?

See help(Sys.sleep), which might be what you want but there may be other
ways in determining if a file is being accessed by another program.

Regards, Adai



On Fri, 2005-07-29 at 12:13 -0700, Tae-Hoon Chung wrote:
> Hi, All;
> 
> I have a question. In R, what is the best way to make R idle for a while
and
> try something again later? For example, suppose there is an R job which
> accesses a file that may be shared with other active jobs. So when the file
> is being accessed by other job, your job will not be able to access the
file
> and your job will crash because of that. To avoid this, you want your job
to
> try to access the file repeatedly with some time interval, say every 10
> seconds or something like that. Which is the best way to do this in R?
> 
> Thanks in advance,
> 
> Tae-Hoon Chung
> 
> Post-Doctoral Researcher
> Translational Genomics Research Institute (TGen)
> 445 N. 5th Street (Suite 530)
> Phoenix, AZ 85004
> 1-602-343-8724 (Direct)
> 1-480-323-9820 (Mobile)
> 1-602-343-8840 (Fax)
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

Dear Tae-Hoon:

1. RSiteSearch('wait') will tell you that Sys.sleep() is what you want.
Although this list is terrific, R's built-in help/search tools should always
be tried first (they're faster when you hit the right search term).

2. The other part of the puzzle is ?try

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box
 
 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Tae-Hoon Chung
> Sent: Friday, July 29, 2005 12:13 PM
> To: RHelp
> Subject: [R] Way to make R idle for some time and try 
> something again later
> 
> Hi, All;
> 
> I have a question. In R, what is the best way to make R idle 
> for a while and
> try something again later? For example, suppose there is an R 
> job which
> accesses a file that may be shared with other active jobs. So 
> when the file
> is being accessed by other job, your job will not be able to 
> access the file
> and your job will crash because of that. To avoid this, you 
> want your job to
> try to access the file repeatedly with some time interval, 
> say every 10
> seconds or something like that. Which is the best way to do this in R?
> 
> Thanks in advance,
> 
> Tae-Hoon Chung
> 
> Post-Doctoral Researcher
> Translational Genomics Research Institute (TGen)
> 445 N. 5th Street (Suite 530)
> Phoenix, AZ 85004
> 1-602-343-8724 (Direct)
> 1-480-323-9820 (Mobile)
> 1-602-343-8840 (Fax)
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

I done something very similar -- have R watch a file, and whenever 
new data is added to the file, read the new data from the file. In my 
case, new data was arriving once per minute, so I needed to have R 
wait about a minute before looking for new data.

On my unix-based system, I found that if I usd
       Sys.sleep( N )
then cpu usage immediately went up drastically. If the the system is 
otherwise fairly idle, cpu usage goes up to nearly 100%. A cpu 
monitor shows that R is using the cpu cycles.

If I use instead
      system('sleep N')
cpu usage does not go up.

(where N is the number of seconds to sleep)
>  version
          _                       
platform powerpc-apple-darwin7.9.0
arch     powerpc                 
os       darwin7.9.0             
system   powerpc, darwin7.9.0    
status                           
major    2                       
minor    1.1                     
year     2005                    
month    06                      
day      20                      
language R                       


At 12:13 PM -0700 7/29/05, Tae-Hoon Chung wrote:
>Hi, All;
>
>I have a question. In R, what is the best way to make R idle for a while and
>try something again later? For example, suppose there is an R job which
>accesses a file that may be shared with other active jobs. So when the file
>is being accessed by other job, your job will not be able to access the file
>and your job will crash because of that. To avoid this, you want your job to
>try to access the file repeatedly with some time interval, say every 10
>seconds or something like that. Which is the best way to do this in R?
>
>Thanks in advance,
>
>Tae-Hoon Chung
>
>Post-Doctoral Researcher
>Translational Genomics Research Institute (TGen)
>445 N. 5th Street (Suite 530)
>Phoenix, AZ 85004
>1-602-343-8724 (Direct)
>1-480-323-9820 (Mobile)
>1-602-343-8840 (Fax)
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA