Andrew Beckerman
2013-Sep-17 11:36 UTC
[R] 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]]
Andrew Beckerman
2013-Sep-19 11:08 UTC
[R] why does system() truncates stdout output from large files? (SOLUTION)
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]]