The Shell

What is the Shell?

The shell (or bash or terminal) is a program on your computer whose job is to run other programs, rather than do calculations itself. The shell is a very old program and in a time before the mouse it was the only way to interact with a computer. It is still extremely popular among programmers because it is very powerful, fast, and is particularly powerful at automating repetitive tasks.

Here we use the shell for a more modest goal: To navigate the file system, confirm the present working directory, and cement the git to GitHub connection.

Starting the shell

In RStudio, go to Tools > Shell. This should take you to the shell (on Mac: Terminal, on Windows: GitBash or equivalent). It should be a simple blinking cursor, waiting for input and looks similar to this (white text on black background, or black text on white background):

Using the shell

The most basic commands are listed below:

• pwd (print working directory). Shows the folder (or directory) you are currently operating in. This is not necessarily the same as the R working directory you get from getwd().
• ls (list all files). Shows all files in the current working directory. This is equivalent to looking at the files in your Finder/Explorer/File Manager. Use ls -a to also list hidden files, such as .Rhistory and .git.
• cd (change directory). Allows you to navigate through your folders by changing the shell’s working directory. You can navigate like so:
  • go to subfolder foo of current working directory: cd foo
  • go to parent folder of current working directory: cd ..
  • go to home folder: cd ~ or simply cd
  • go to folder using absolute path, works regardless of your current working directory: cd /home/my_username/Desktop. Windows uses a slightly different syntax with the slashes between the folder names reversed, \, e.g. cd C:\Users\MY_USERNAME\Desktop.
  • Pro tip 1: Dragging and dropping a file or folder into the terminal window will paste the absolute path into the window.
  • Pro tip 2: Use the tab key to autocomplete unambiguous folder and file names. Hit tab twice to see all ambiguous options.
• Use arrow-up and arrow-down to repeat previous commands. Or search for previous commands with CTRL+r.
• git status is the most used git command and informs you of your current branch, any changes or untracked files, and whether you are in sync with your remotes.
• git remote -v lists all remotes. Very useful for making sure git knows about your remote and that the remote address is correct.
• git remote add origin GITHUB_URL adds the remote GITHUB_URL with nickname origin.
• git remote set-url origin GITHUB_URL changes the remote url of origin to GITHUB_URL. This way you can fix typos in the remote url.

Go back to the index for the all the Git stuff.