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sprintf in system command

3 messages · Esam Tolba, jim holtman, Rui Barradas

Esam Tolba
# 
hi all
I am using r (2.15.2) in windows 7 32bit
I want to execute an external program from r console. the program is a
command line program which needs the following format to start
                                  C:/Users/.../dssp-2.0.4-win32.exe -i
data_1.txt -o data_1.dssp
I used the system command as:
                                  system
('C:/Users/.../dssp-2.0.4-win32.exe -i data.txt -o data.dssp')
it worked.
Now I want to use the program on a list of files, so for that I used a
for loop and sprintf
                                   for (i in 1:10) {
                                   system
('C:/Users/.../dssp-2.0.4-win32.exe -i sprintf("data_%s.txt",i) -o
sprintf("data_%s.dssp",i)')
but I received the following error
                    No such file
                    Warning message:
                    running command 'C:/Users/.../dssp-2.0.4-win32.exe
-i sprintf("data_%s.txt",i) -o sprintf("data_%s.dssp",i)' had status 1


SO, what is my mistake? and is there a way to update the input file
name based on  the for loop counter

Best Regards,
jim holtman
# 
I think what you want is something like this

 system(sprintf('C:/Users/.../dssp-2.0.4-win32.exe -i data%d.txt -o
data%d.dssp', i, i))
On Fri, Feb 15, 2013 at 12:33 PM, Esam Tolba <eatolba at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
      #
    

  


  

      
Hello,

In what follows I've used print(), not system().
The trick is to use paste0() to form the command.


for (i in 1:10) {
	cmd <- paste0('C:/Users/.../dssp-2.0.4-win32.exe -i ', 
sprintf("data_%s.txt",i), ' -o ', sprintf("data_%s.dssp",i))
	print(cmd)
}


Hope this helps,

Rui Barradas

Em 15-02-2013 17:33, Esam Tolba escreveu: