R help - Mar 2013 - Help using system() command to execute Perl script through MSDOS

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











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On Mar 6, 2013, at 8:52 PM, pdbarry <pdbarry at 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