Chapter 1 Introduction

1.1 What is Shell/Terminal?

Shell is a text based application for viewing, handling & manipulating files. It takes in commands and passes them on to the operating system. It is also known as

  • CLI (Command Line Interface)
  • Bash (Bourne Again Shell)
  • Terminal

It is sufficient to know a handful of commands to get started with the shell.

1.2 Launch Terminal

Although we will use the terminal in RStudio on RStudio Cloud, we should still know how to launch the terminal in different operating systems.

1.2.1 mac

Applications -> Utility -> Terminal

1.2.2 Windows

1.2.2.1 Option 1

Go to the Start Menu or screen and enter Command Prompt in the search field.

1.2.2.2 Option 2

Start Menu -> Windows System -> Command Prompt

1.2.2.3 Option 3

Hold the Windows key and press the R key to get a Run window. Type cmd in the box and click on the OK button.

1.2.3 Linux

  • Applications -> Accessories -> Terminal
  • Applications -> System -> Terminal

1.2.4 Windows Subsystem for Linux

If you want to use bash on Windows, try the Windows subsystem for Linux. It only works on 64 bit Windows 10. Below are the steps to enable Windows subsystem fro Linux:

1.2.4.1 Step 1 - Enable Developer Mode

To enable Developer Mode open the Settings app and head to Update & Security > For Developers. Press the Developer Mode switch.

1.2.4.2 Step 2 - Enable Windows Subsystem for Linux

To enable the Windows Subsystem for Linux (Beta), open the Control Panel, click Programs and Features, and click Turn Windows Features On or Off in left side bar under Programs and Features. Enable the Windows Subsystem for Linux (Beta) option in the list here and click OK. After you do, you’ll be prompted to reboot your computer. Click Restart Now to reboot your computer and Windows 10 will install the new feature.

1.2.4.3 Step 3 - Install your Linux Distribution of Choice

Open the Microsoft store and choose your favorite Linux distribution.

In the distro’s page, click on “Get”.

Launch the distro from the Start Menu.

You can learn more about the Windows Subsystem for Linux here.

1.2.5 RStudio Terminal

RStudio introduced the terminal with version 1.1.383. The terminal tab is next to the console tab. If it is not visible, use any of the below methods to launch it

  • Shift + Alt + T
  • Tools -> Terminal -> New Terminal

Note, the terminal depends on the underlying operating system. To learn more about the RStudio terminal, read this article or watch this webinar. In this book, we will use the RStudio terminal on RStudio Cloud to ensure that all users have access to Linux bash. You can try all the commands used in this book on your local system as well except in case of Windows users.

1.3 Prompt

As soon as you launch the terminal, you will see the hostname, machine name and the prompt. In case of mac & Linux users, the prompt is $. For Windows users, it is >.

OS Prompt
macOS $
Linux $
Windows >

1.4 Get Started

To begin with, let us learn to display

  • basic information about the user
  • the current date & time
  • the calendar
  • and clear the screen.
Command Description
whoami Who is the user?
date Get date, time and timezone
cal Display calendar
clear Clear the screen

whoami prints the effective user id i.e. the name of the user who runs the command. Use it to verify the user as which you are logged into the system.

## aravind

date will display or change the value of the system’s time and date information.

## Tue Oct 22 14:56:56 IST 2019

cal will display a formatted calendar and clear will clear all text on the screen and display a new prompt. You can clear the screen by pressing Ctrl + L as well.

##     October 2019      
## Su Mo Tu We Th Fr Sa  
##        1  2  3  4  5  
##  6  7  8  9 10 11 12  
## 13 14 15 16 17 18 19  
## 20 21 _2_2 23 24 25 26  
## 27 28 29 30 31        
## 

In R, we can get the user information from Sys.info() or whoami() from the whoami package. The current date & time are returned by Sys.date() & Sys.time(). To clear the R console, we use Ctrl + L.

Command R
whoami Sys.info() / whoami::whoami()
date Sys.date() / Sys.time()
cal
clear Ctrl + L

1.5 Help/Documentation

Before we proceed further, let us learn to view the documentation/manual pages of the commands.

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

man is used to view the system’s reference manual. Let us use it to view the documentation of the whatis command which we will use next.

## WHATIS(1)                     Manual pager utils                     WHATIS(1)
## 
## NAME
##        whatis - display one-line manual page descriptions
## 
## SYNOPSIS
##        whatis  [-dlv?V]  [-r|-w]  [-s  list]  [-m  system[,...]] [-M path] [-L
##        locale] [-C file] name ...
## 
## DESCRIPTION
##        Each manual page has a short description available within  it.   whatis
##        searches  the  manual  page names and displays the manual page descrip‐
##        tions of any name matched.
## 
##        name may contain wildcards (-w) or be a regular expression (-r).  Using
##        these  options, it may be necessary to quote the name or escape (\) the
##        special characters to stop the shell from interpreting them.
## 
##        index databases are used during the search,  and  are  updated  by  the
##        mandb  program.   Depending  on your installation, this may be run by a
##        periodic cron job, or may need to be  run  manually  after  new  manual
##        pages  have  been installed.  To produce an old style text whatis data‐
##        base from the relative index database, issue the command:
## 
##        whatis -M manpath -w '*' | sort > manpath/whatis
## 
##        where manpath is a manual page hierarchy such as /usr/man.
## 
## OPTIONS
##        -d, --debug
##               Print debugging information.
## 
##        -v, --verbose
##               Print verbose warning messages.
## 
##        -r, --regex
##               Interpret each name as a regular expression.  If a name  matches
##               any  part  of  a  page  name, a match will be made.  This option
##               causes whatis to be somewhat slower due to the nature  of  data‐
##               base searches.
## 
##        -w, --wildcard
##               Interpret  each  name  as a pattern containing shell style wild‐
##               cards.  For a match to be made, an expanded name must match  the
##               entire  page  name.   This  option  causes whatis to be somewhat
##               slower due to the nature of database searches.
## 
##        -l, --long
##               Do not trim output to the terminal width.  Normally, output will
##               be  truncated  to  the terminal width to avoid ugly results from
##               poorly-written NAME sections.
## 
##        -s list, --sections list, --section list
##               Search only the given manual sections.   list  is  a  colon-  or
##               comma-separated list of sections.  If an entry in list is a sim‐
##               ple section,  for  example  "3",  then  the  displayed  list  of
##               descriptions  will include pages in sections "3", "3perl", "3x",
##               and so on; while if an entry in list has an extension, for exam‐
##               ple "3perl", then the list will only include pages in that exact
##               part of the manual section.
## 
##        -m system[,...], --systems=system[,...]
##               If this system has access to  other  operating  system's  manual
##               page  names,  they can be accessed using this option.  To search
##               NewOS's manual page names, use the option -m NewOS.
## 
##               The system specified can be a  combination  of  comma  delimited
##               operating system names.  To include a search of the native oper‐
##               ating system's manual page names, include the system name man in
##               the  argument  string.   This  option  will override the $SYSTEM
##               environment variable.
## 
##        -M path, --manpath=path
##               Specify an alternate set of colon-delimited manual page  hierar‐
##               chies  to search.  By default, whatis uses the $MANPATH environ‐
##               ment variable, unless it is empty or unset,  in  which  case  it
##               will  determine an appropriate manpath based on your $PATH envi‐
##               ronment variable.  This option overrides the contents  of  $MAN‐
##               PATH.
## 
##        -L locale, --locale=locale
##               whatis  will normally determine your current locale by a call to
##               the C function setlocale(3) which interrogates various  environ‐
##               ment  variables,  possibly including $LC_MESSAGES and $LA

whatis displays short manual page descriptions (each manual page has a short description available within it).

## ls (1)               - list directory contents

You will find tldr.sh very useful while exploring new commands and there is a related R package, tldrrr as well.

## pwd 
##  
## Print name of current/working directory. 
##  
## • Print the current directory: 
##  
##   pwd 
##  
## • Print the current directory, and resolve all symlinks (i.e. show the "physical" path): 
##  
##   pwd -P