Installing Command Line Tools
A command-line interface or command language interpreter (CLI), also known as a terminal, is a means of interacting with a computer program where the user issues commands to the program in the form of successive lines of text (command lines).
Throughout the course we will emphasize use of the terminal and executing commands within it as our modus operandi.
So that we can work as closely as possible to the Mac and Linux users we will install Cygwin.
- Download Cygwin here and use the graphical installer. Accept all the default options.
- Choose any server from which to download cygwin and packages when prompted.
- Verify your installation by opening Cygwin. When it opens you should see a black box with some text that looks like:
We will uses Cygwin as our command line tool, and unlike other Windows shells such as PowerShell it uses Unix syntax.
Anywhere throughout the remainder of the installation guide where we suggest you to enter a command into a terminal, enter the text-based command into your Cygwin terminal followed by pressing
Return, for example:
userName@computerName: ~$ whoami
Should return your username.
Do not delete the setup-x86_64.exe file. It needs to be kept so that we can add on some additional packages to use in the course.
A command line interface comes already installed with MacOS.
You will need to install some other software from the terminal thoughout the course, so it will be useful to install some additional “command line tools” now:
- First we want to install X-code command line tools. Open a terminal by searching for it with spotlight,
cmd + spacebarthen type terminal and press
Returnwhen it appears. Then, copy and paste the following
If you get an answer that the command line tools are already installed, you can just continue to the next step.
- Second, install Homebrew by opening a terminal and pasting the following command:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/homebrew/install/master/install)"
- To verify that Homebrew installed correctly, enter the following into your terminal
And you should see the following output
Your system is ready to brew
- Now we can use Homebrew to easily install software. To use the current R version 3.5.1, we want to make sure you have some basic system tools that some packages require. Let’s (re)install them real quick. First
brew reinstall libxml2
If you system tells you that it is not yet installed, then try
brew install libxml2 instead.
We also want to link this so that terminal finds it later:
echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile
- Second, we also need
brew reinstall openssl
Again, if it is already installed, then use
brew install openssl instead.
Again, we need it to link to terminal:
echo 'export PATH="/usr/local/opt/openssl/bin:$PATH"' >> ~/.bash_profile
- Finally, we need
brew install libgit2
If terminal tells you it is not yet installed, then go for
brew reinstall libgit2
To use the current R version, we need to install some system tools. For this open a terminal session with
- Now copy the following command into terminal and press
sudo apt-get install libcurl4-gnutls-dev librtmp-dev
- After the installation succeeded successfully repeat this one-by-one with the following two other commands:
sudo apt-get install libxml2-dev sudo apt-get install libssl-dev