On Mar 6, 2013, at 8:52 PM, pdbarry <pdba...@alaska.edu> wrote:
> I am working on creating a program for some simulations I need to do and I
> want to execute a Perl script that I wrote using the system() command in R.
> I have spent a couple days trying to figure this out and it appears that my
> problem occurs when sending the perl script file path through R to MSDOS. I
> have tried using double backslashes, quotations, etc. Moving my files to the
> root directory with no folders with spaces seems to make the problem go
> away.
>
> So here is the code:
> system(paste("perl",FP.chmod,FP.baseline.in,FP.baseline.out))
>
> where perl is the command to use the perl script
> FP.chmod is the extenstion to the perl file
> "C:/Documents and Settings/Pato/Desktop/Mikes R package/chmod700.pl"
> created using FP.chmod<- file.path(wd,'chmod700.pl') #wd is the
> working directory
> FP.baseline.in is the input file extension
> "C:/Documents and Settings/Pato/Desktop/Mikes R
> package/Baseline2c.bse"
> FP.baseline.out is the output to make from the perl script.
>
> If I look at it pasted together it looks like it would work:
> "perl C:/Documents and Settings/Pato/Desktop/Mikes R package/chmod700.pl
> C:/Documents and Settings/Pato/Desktop/Mikes R package/Baseline2c.bse
> C:/Documents and Settings/Pato/Desktop/Mikes R package/Baseline2d.bse
>
> If I change the location of the files so that they are directly under the
> root directory it runs without a hitch. I greatly appreciate any help that
> can be offered.
> Pat
You might want to take a look to see how I do it in WriteXLS():
https://github.com/marcschwartz/WriteXLS/blob/master/R/WriteXLS.R
Look at around line 167 in the R source.
The key thing to understand (as you hint at above) is that spaces in the
arguments on the CLI are delimiters, separating what you have as a single
argument into multiples.
Use ?shQuote to put single quotes around each argument that contains spaces, so
that it is treated as a single argument:
> shQuote("This is a single argument")
[1] "'This is a single argument'"
Regards,
Marc Schwartz
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