Question

I am testing out the bio3d package in R (Windows) and encountered a rather general problem:

The “seqaln” function in bio3d tries to issue the following system command:

#cmd = "muscle -in C:\\Users\\derek\\AppData\\Local\\Temp\\RtmpUSXJCb\\file756f52c9 -out c:/pdb/temp.fas  -seqtype protein"
system(shQuote(cmd))

As far as I can tell, nothing happened. However, once I removed the “shQuote”, the function – seqaln – worked as expected. All shQuote does is added a pair of “” around the command:

"\"C:/_utils/muscle.exe -in C:\\Users\\kfoo\\AppData\\Local\\Temp\\RtmpUSXJCb\\file756f52c9 -out c:/pdb/temp.fas  -seqtype protein\""

Is there something wrong with using shQuote?

Thanks!

Answer 1

The problem is that you are applying shQuote() to a character string that contains both a command and it’s arguments. None of the examples in shQuote() does that, and neither should you!

The following doesn’t work, for the same reason that \"echo HelloWorld\" fails when typed directly at Windows’ cmd command line:

system(shQuote("echo HelloWorld"))

Instead, you should do the following:

system("echo HelloWorld")
# HelloWorld

Or, if both your command and its argument may contain spaces, you can use shQuote() like this:

system(paste(shQuote("echo"), shQuote("HelloWorld")))
# HelloWorld