Execute perl script with arguments in R

Question

I have a perl script (SFDRv166.pl, available here http://bit.ly/1DGmUTL) that I run successfully from the command line using:

perl SFDRv166.pl -assoc input.txt -SFDR -out test

I now need to run this program as part of an R script, and have tried implementing it as follows:

arg1 <- shQuote("-assoc input.txt")
arg2 <- shQuote("-SFDR")
arg3 <- shQuote("-out test")

system("perl SFDRv166.pl arg1 arg2 arg3")

However, I get an ERROR: cannot find ! message generated I believe because the arguments are not getting passed to the perl script (output says no input or output file specified, and no output is created).

I can see from reading the documentation for system() that arguments with spaces require special handling, which is why I have tried to use shQuote(). Not sure what else may be wrong with my approach?

Use paste: system(paste("perl","SFDRv166.pl",arg1,arg2,arg3)) — nicola
– nicola, Commented Apr 7, 2015 at 12:18
Look at the source for xls2sep in the gdata package. It calls perl with arguments. — G. Grothendieck
– G. Grothendieck, Commented Apr 7, 2015 at 12:28

pogibas · Accepted Answer · 2015-04-07 12:18:59Z

2

Try this:

arg1 <- "-assoc input.txt"
arg2 <- "-SFDR"
arg3 <- "-out test"
cmd <- paste("perl", "SFDRv166.pl", arg1, arg2, arg3)
system(cmd)

Now you don't need shQuate.

answered Apr 7, 2015 at 12:18

pogibas

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