R help - Sep 2013 - why does system() truncates stdout output from large files?

Dear listers  

I am using a system() call to my machine (OSX 10.8, R 3.0.1. 32GB memory
available):

system(paste("awk 'NR==2'", file.genepop), intern = TRUE)

and when processing big files, getting numerous helpful error messages

system(paste("awk 'NR==2'", file.genepop), intern = TRUE,  ...
:
  line 1 may be truncated in call to system(, intern = TRUE)

I understand what is happening, and can see the truncations, but is there any
way to prevent the truncation?  Or is there a read-limit in system() [I
can't see anything in the help file… but I am probably missing something]?

Many thanks
Andrew


--  
Andrew Beckerman
University of Sheffield



	[[alternative HTML version deleted]]

Dear all -  

Should anyone be interested - using  

paste(system(paste("awk 'NR==2'", file.genepop), intern =
TRUE), collapse="")

pulls together the pieces (list elements) of the returned values.

--  
Andrew Beckerman
University of Sheffield


On Tuesday, 17 September 2013 at 12:36, Andrew Beckerman wrote:
> Dear listers  
>  
> I am using a system() call to my machine (OSX 10.8, R 3.0.1. 32GB memory
available):
>  
> system(paste("awk 'NR==2'", file.genepop), intern = TRUE)
>  
> and when processing big files, getting numerous helpful error messages
>  
> system(paste("awk 'NR==2'", file.genepop), intern = TRUE,
... :
>   line 1 may be truncated in call to system(, intern = TRUE)
>  
> I understand what is happening, and can see the truncations, but is there
any way to prevent the truncation?  Or is there a read-limit in system() [I
can't see anything in the help file… but I am probably missing something]?
>  
> Many thanks
> Andrew
>  
>  
> --  
> Andrew Beckerman
> University of Sheffield
>  
>  

	[[alternative HTML version deleted]]