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.

Windows Users

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:
userName@computerName: ~$

i.e. for Uli he sees:

ubergmann@dhcp-wlan-uzh-10-12-130-xxx: ~$

We will explain what all this means in the first day or so of the course.

Why Cygwin

  • 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 Install File

  • 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.

Mac Users

A command line interface comes already installed with OSX.

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 + spacebar then type terminal and press Return when it appears. Then, copy and paste the following
xcode-select --install

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
brew doctor

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 libxml2:
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 openssl:
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 libgit2:
brew install libgit2

If terminal tells you it is not yet installed, then go for brew reinstall libgit2

Linux Users

To use the current R version, wee need to install some system tools. For this open a terminal session with Crtl + Alt + T.

  • Now copy the following command into terminal and press Enter:
  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