R中的带引号的mac shell命令

Question

I am using RStudio on Mac. I want to execute a shell command (terminal command) from within a R script file. I am using the system function in R to do this.

However, to take a step further, I have a shell command that has a loop and passes some parameters. To pass these parameters, I need to use quote marks. As system function already takes quotes, these second set of quotes are giving a syntax error. For example

1. simple call @ terminal : mkdir ch; when translated to R will be

   system("mkdir ch")

in Rscript makes a ch folder in workspace.

2. loop call @ terminal =

   for file in *.pdf; do pdftotext "$file" "$file.txt"; done.

in terminal the above command will loop the 'pdftotext' command on each file in the directory. But as you notice, this call already has quotes (file variable) and conflicts with quotes of system("") function in R

How can I do this shell command with a loop call into R system function?

Answer 1

The problem is that once you include a second double quote, you're telling R to close the string. Take this sample string as an example:

x = "I use air "quotes" like this..."
# Error: unexpected symbol in "x = "I use air "quotes"

It doesn't like the embedded double quotes. But, if we replace the double quotes with single quotes, our problem goes away:

x = 'I use air "quotes" like this...' # or
x = "I use air 'quotes' like this..."

Either way, the two types of quotes essentially ignore each other and all is well. However, sometimes that's not enough. What if you have embedded quotes inside of embedded quotes?

x = "python some_syntax.py '["Me", "You", "Him"]'"
# Error: unexpected symbol in "x = "python some_syntax.py '["Me"

We can fix this problem by escaping quotes with a backslash. I'm going to reverse where I use single and double quotes, though, to minimize the number of escapes needed.

x = "python some_syntax.py \"['Me', 'You', 'Him']\""

Again, all is well.

Hope that helps.