Running a Windows executable file from within R with command line options
call, executable, external, r
Solution
You've heard of `bquote` , `noquote` , `sQuote`, `dQuote` , `quote` `enquote` and `Quotes`, well now meet `shQuote`!!! :-)
This little function call works to format a string to be passed to an operating system shell. Personally I find that I can get embroiled in backslash escaping hell, and `shQuote` saves me. Simply type the character string as you would on the command line of your choice (`'sh'` for Unix alikes like `bash` , `csh` for the C-shell and `'cmd'` for the Windows shell ) wihtin `shQuote` and it will format it for a call from `R` using system:
shQuote("C:/NIST08/AMDIS32/AMDIS_32.exe /S C:/Users/Ento/Documents/GCMS/test_cataglyphis_iberica/queens/CI23_Q_120828_01.CDF" , type = "cmd" )
#[1] "\"C:/NIST08/AMDIS32/AMDIS_32.exe /S C:/Users/Ento/Documents/GCMS/test_cataglyphis_iberica/queens/CI23_Q_120828_01.CDF\""
More generally, you can use `shQuote` like this:
system( shQuote( "mystring" , type = c("cmd","sh") ) , ... )
Problem
I am trying to call a Windows program called AMDIS from within R using the call ``` system("C:/NIST08/AMDIS32/AMDIS_32.exe /S C:/Users/Ento/Documents/GCMS/test_cataglyphis_iberica/queens/CI23_Q_120828_01.CDF") ``` in order to carry out an analysis (specified using the `/S` switch) on a file called `CI23_Q_120828_01.CDF`, but it seems that no matter what I try the file is not loaded in correctly, presumably because the options are not passed along. Does anyone have a clue what I might be doing wrong? Right now this command either - doesn't do anything, - makes AMDIS pop up, but it doesn't load the file I specify gives me the error Warning message: running command 'C:/NIST08/AMDIS32/AMDIS_32.exe /S C:/Users/Ento/Documents/GCMS/test_cataglyphis_iberica/queens/CI23_Q_120828_01.CDF' had status 65535 (I have no idea what results in these different outcomes of the same command) (the AMDIS command line options are described here at the page 8) Cheers, Tom EDIT: Found it had to do with forward vs backslashes - running ``` system("C:\\NIST08\\AMDIS32\\AMDIS_32.EXE C:\\Users\\Ento\\Documents\\GCMS\\test_cataglyphis_iberica\\queens\\CI23_Q_120828_01.CDF /S /E") ``` seems to work - thank you all for the suggestions!