Terminal

Shell is an application that allows you to communicate directly with the operating system via code rather than pointing and clicking. It takes commands via text, and is often used for viewing, editing, and handling files, advanced source control operations, or execution of long-running jobs.

Shell/Terminal is also known as CLI (Command Line Interface) or Bash (Bourne Again Shell). It predates graphical user interfaces (GUI), but remains superior in some areas of functionality and efficiency.

The terminal in RStudio also allows you to access the system shell, but the terminal can also be launched from Applications on Mac, or as Command Prompt on Windows.

Using the Terminal in RStudio

You can access the R Terminal through the ‘terminal’ tab near the console

If the tab is not already showing: Tools -> Terminal -> New Terminal

You can have multiple terminal sessions simultaneously using the ‘New Terminal’ option, and switch between them using the arrows in the top left

Terminals can be closed with the ‘X’ or with the ‘close terminal’ option

Helpful Commands

Command	Description
whoami	Who is the user?
cdate / date	Get date, time and timezone
cal	Display calendar
clear	Clear the screen

The clear command clears only the visible part of the terminal; to fully wipe it, use Ctrl+L.

View Documentation

Command	Description
man	Display manual pages for a command
whatis	Single line description of a command

Check or Change Working Directory

Command	Description
pwd	Print working directory
ls	List directory contents
cd	Change current working directory
mkdir	Create directory
rmdir	Remove/delete directory

Managing Files

Command	Description
touch	Create empty file(s)/change timestamp
cp	Copy files & folders
mv	Rename/move file
rm	Remove/delete file
diff	Compare files

If the file does not exist, touch will create an empty file of the given name:

touch myanalysis.R

We can create a copy of a file called release_names.txt and name it release_names_2.txt with the following:

cp release_names.txt release_names_2.txt

Running R Code in Terminal

R -e will launch R and then run the code specified within quotes. Use a semi-colon to execute multiple expressions. Windows users must ensure that R is added to the path environment.

R -e "head(mtcars); tail(mtcars)"

Rscript -e will run code without launching R, or execute an R script (.R file):

Rscript -e "head(mtcars)"

Rscript analysis.R

While editing files in RStudio, the current line or selected lines can be sent to the active terminal via Ctrl+Alt+Enter/Cmd+Opt+Return (on a Mac).

Programs can be running in the Terminal and in RStudio simultaneously.

Running R Code on a Remote Server

If you are working with data that is too large or your analysis requires too much memory, you may need to access a remote server. We can do so with ssh or secure shell.

In a Terminal, the most straightforward way to access a remote server is with the ssh command and connecting to the IP address or domain name of the remote_host with your assigned username.Ma

ssh username@remote_host

You’ll need to provide a password to ensure you have proper authorization to access that server. Once you have access to that machine, you may run commands just as you might work in the Terminal on your local machine.

To quit/exit, the remote server, type

exit

At Macalester, you could practice this by logging into the MSCS remote server.

If you are on campus (or are currently running only a Mac VPN), you can open the Terminal and type (use your Mac username)

ssh username@mscs.olri.macalester.edu

and provide your Mac password (same as email, 1600Grand, etc.).

Try the following commands to create new folders and files and navigate through those folders:

pwd
mkdir DS212
ls
cd DS212
mkdir homework
cd homework
touch hw1.txt
exit

This server does not have R installed so the R commands won’t work on this server but they could work on another server that did have R installed.

Transfering files to/from a Remote Server

If you are wanting to copy files from your local machine to a remote server,

scp file.txt username@remote_host:remote_path

If you are wanting to copy files from a remote server to your local machine,

scp username@remote_host:remote_path/file.txt local_path