Using `diff` from R via `system(..)`

问题

I was willing to compare two paths (named a and b) in R using the diff command from Bash.

In bash I would do

$ a=Path/to/foo/directory/
$ b=Path/to/bar/directory/
$ diff <(printf ${a} | tr / '\n') <(printf ${b} | tr / '\n')
3c3
< foo
---
> bar

So from R I am trying

a="Path/to/foo/directory/"
b="Path/to/bar/directory/"
system(
  paste0(
    "a=",a,
    ";b=",b,
    ";diff <(printf ${a} | tr / '\n') <(printf ${b} | tr / '\n')"
  )
)

system(
    paste0(
      "diff <(printf ",a," | tr / '\n') <(printf ",b," | tr / '\n')"
    )
  )

but both return an error.

sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `a=Path/to/foo/directory/;b=Path/to/bar/directory/;diff <(printf ${a} | tr / ''

even though copy-pasting the output of the paste0 function into bash works fine.

There might be better ways to compare strings in R and I would welcome alternative solutions. However, I am particularly interested in understanding what is going wrong with my usage of the system() function and how to solve it.

回答1:

As explained here, system(..) is not running /usr/bin/bash but /usr/bin/sh. Here are two possible solutions to the problem.

Solution in "usr/bin/sh"

So in order to make a script that run through /usr/bin/sh I had to print strings on files.

DiffPath = function(a,b,ManipulationFolder="~")
{
  if (file.exists(ManipulationFolder))
  {
  system(
    paste0(
      "cd ",ManipulationFolder,
      ";a=",a,
      ";b=",b,
      ";printf ${a} | tr / '\n' > a.txt",
      ";printf ${b} | tr / '\n' > b.txt",
      ";diff a.txt b.txt",
      ";rm a.txt;rm b.txt"
    )
  ) 
  } else
  {
    warning(paste0("Cannot find the ManipulationFolder ( ",ManipulationFolder," )"))
  }
}

Solution in "usr/bin/bash"

An alternative and nicer solution is to explicitly give the command to bash.

DiffPath = function(a,b)
{
  system(
    paste0(
      'bash -c \'diff <(printf ',a,' | tr / "\n") <(printf ',b,' | tr / "\n")\''
    )
  ) 
}

Function call

a="Path/to/foo/directory/"
b="Path/to/bar/directory/"

DiffPath(a,b)
3c3
< foo
---
> bar

来源：https://stackoverflow.com/questions/39128344/using-diff-from-r-via-system

标签

string

bash

diff