通过`system（..）`使用R中的`diff` [英] Using `diff` from R via `system(..)`

问题描述

我愿意比较 R中的两个路径（分别命名为 a 和 b ） ，使用 Bash 中的 diff 命令。

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

在bash中我会做

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

所以从RI正在尝试

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')"
  )
)

OR

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

，但都返回错误。

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 / ''

即使复制粘贴了输出在bash中使用 paste0 函数可以正常工作。

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

在R中比较字符串可能会有更好的方法，我也欢迎使用替代方法解决方案，但是，我参与其中对了解我对 system（）函数的用法有什么问题以及如何解决它很感兴趣。

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.

推荐答案

如此处，系统（..）未运行 / usr / bin / bash ，但 / usr / bin / sh 。这是解决该问题的两种可能的解决方案。

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

usr / bin / sh中的解决方案

因此，要使脚本通过 / usr / bin / sh 运行，我必须在文件上打印字符串。

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," )"))
  }
}

usr / bin / bash中的解决方案

一种更好的选择解决方案是显式地执行bash命令。

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")\''
    )
  ) 
}

函数调用

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

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

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