[R] paste? 'cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1'

[Boks, M.P.M.]

Dear R users,
 
This command works (calling a programm -called whap- with file specifiers etc.):
 
system('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1 --perm 500', 
intern=TRUE)
 
Now I need to call it from a loop to replace the 1 by different number, 
however I get lost using the quotes:
 
I tried numerous versions of:
 
i-1
system(paste(c('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt, i,  
--perm 500', sep= )), intern=TRUE)
 
However no luck! I would be gratefull for any help.
 
Thanks,
 
Marco

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Re: [R] paste? 'cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1'

[Marc Schwartz (via MN)]

On Mon, 2006-09-25 at 18:58 +0200, Boks, M.P.M. wrote:
 Dear R users,
  
 This command works (calling a programm -called whap- with file specifiers 
 etc.):
  
 system('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1 --perm 500', 
 intern=TRUE)
  
 Now I need to call it from a loop to replace the 1 by different number, 
 however I get lost using the quotes:
  
 I tried numerous versions of:
  
 i-1
 system(paste(c('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt, i,  
 --perm 500', sep= )), intern=TRUE)
  
 However no luck! I would be gratefull for any help.
  
 Thanks,
  
 Marco

You need to escape the quote () chars in the paste()d string so that
they get passed to your command properly. Also, you don't want to use
c() within the paste() function, as the paste() function already
concatenates the component vectors.

Note:

i - 1

 paste('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt, i,   --perm 
 500', sep=)
Error: syntax error in paste('cmd /c c

R sees the double quote before the second 'c' as the end of the string:

  'cmd /c 


Now use \ to escape the internal quotes:

 paste('cmd /c \c:\\pheno\\whap --file c:\\pheno\\smri --alt , i,   --perm 
 500\', sep=)
[1] 'cmd /c \c:\\pheno\\whap --file c:\\pheno\\smri --alt 1 --perm 500\'


Use '\' to escape each of the double quotes within the string, so that R
can differentiate string delimiters versus characters within the string.

HTH,

Marc Schwartz

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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.

Re: [R] paste? 'cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1'

[Gabor Grothendieck]

Use single outer quotes so that the inner double quotes are not
interpreted as the end of the string.

cmd - 'cmd /c ...whatever... '
system(cmd, intern = TRUE)

On 9/25/06, Boks, M.P.M. [EMAIL PROTECTED] wrote:
 Dear R users,

 This command works (calling a programm -called whap- with file specifiers 
 etc.):

 system('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt 1 --perm 500', 
 intern=TRUE)

 Now I need to call it from a loop to replace the 1 by different number, 
 however I get lost using the quotes:

 I tried numerous versions of:

 i-1
 system(paste(c('cmd /c c:\\pheno\\whap --file c:\\pheno\\smri --alt, i,  
 --perm 500', sep= )), intern=TRUE)

 However no luck! I would be gratefull for any help.

 Thanks,

 Marco

 __
 R-help@stat.math.ethz.ch mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.