R help - Aug 2011 - R system command does not work with objects/variables

Hello!

with the R system command I would like to call a perl script which needs an
input directory and an output directory in form of a path. When I put in the
path directly it works. The script line looks as follows:

system("perl '../path1' '../path2'
'../path3'")
	
If I store the path in a variable/object and call the perl script again it
does not run and I don't know how to overcome that issue.

p1 <- "../path1"
p2 <- "../path2"
p3 <- "../path3"

system("perl p1 p2 p3")

I also tried:

system("perl 'p1' 'p2' 'p3'")

Can anyone help?

Best,
syrvn

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See ?paste
or use system2("perl", shQuote(c(p1, p2, p3)))

On Tue, 23 Aug 2011, syrvn wrote:
> Hello!
>
> with the R system command I would like to call a perl script which needs an
> input directory and an output directory in form of a path. When I put in
the
> path directly it works. The script line looks as follows:
>
> system("perl '../path1' '../path2'
'../path3'")
>
> If I store the path in a variable/object and call the perl script again it
> does not run and I don't know how to overcome that issue.
>
> p1 <- "../path1"
> p2 <- "../path2"
> p3 <- "../path3"
>
> system("perl p1 p2 p3")
>
> I also tried:
>
> system("perl 'p1' 'p2' 'p3'")
>
> Can anyone help?
>
> Best,
> syrvn
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/R-system-command-does-not-work-with-objects-variables-tp3762544p3762544.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Hi,

it works great with the paste command! thanks a lot!

Best,
syrvn

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View this message in context:
http://r.789695.n4.nabble.com/R-system-command-does-not-work-with-objects-variables-tp3762544p3762583.html
Sent from the R help mailing list archive at Nabble.com.

syrvn <mentor_ at gmx.net> writes:
> If I store the path in a variable/object and call the perl script again it
> does not run and I don't know how to overcome that issue.
>
> p1 <- "../path1"
> p2 <- "../path2"
> p3 <- "../path3"
>
> system("perl p1 p2 p3")
You want something like:

  system(paste("perl", p1, p2, p3"))

Strings don't do interpolation by themselves; you need to tell R, via
the "paste" function, that you want to concatenate the strings
together.

-Johann