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Essential preparation for the Vacation School: Set up your laptop

[Note to participants who are looking for introductory R tutorial material online, ahead of the Vacation School: Please see the suggested links under "Target audience" on the Vacation School homepage.]


Participants are encouraged to bring their own laptops to the WDSI Vacation School. Laptops should have the following installed prior to attending the vacation school:

  • R (3.4.1)
  • RStudio (1.0.143 or later)

If you have older versions of R/RStudio installed, it is recommended that you install the latest versions. Instructions on installing R and RStudio are given below.

Participants not attending the half-day introduction to R should also install the following CRAN packages and their dependencies:

  • dplyr
  • ggplot2
  • knitr
  • rmarkdown
  • rio
  • tidyr

Please ensure that you have the latest versions of these packages installed. The exact mechanism for installing packages will depend on your computer's operating system. If you cannot see how to do it, please ask a friend or post a question to the Vacation School Forum.

Optional:

Also below are some instructions for installing LaTeX, and installing additional tools to compile packages from source code (the so-called development tools). These tools will be referred to in the course, but are not required for the Vacation School computing labs.

Installing R

Download the pre-compiled binary for your OS from https://cloud.r-project.org/ and install. More specifically:

For Windows

Click “Download R for Windows”, then “base”, then “Download R 3.4.1 for Windows”. This will download an .exe file; once downloaded, open to start the installation. If you do not have administrator rights, the installer will default to install in your Documents folder. If you prefer, you can change the location to another folder that you have write access to. (It is preferable to install R in a location to which you have full access, rather than needing administrator privileges).

For Mac

Click “Download R for (Mac) OS X”, then “R-3.4.1.pkg” to download the installer. Run the installer to complete installation.

For Linux

Click “Download R for Linux”. Instructions on installing are given for Debian, Redhat, Suse and Ubuntu distributions. Where there is a choice, install both r-base and r-base-dev.

Installing RStudio

Downloads are available from https://www.rstudio.com/products/rstudio/download3/ (scroll to the end of the page to see the downloads).

For Windows with no admin rights

Download the .zip source archive. Extract the files to a folder where you have write access, e.g. C:\Users\username\RStudio. In this folder, open the bin directory and find the RStudio program: it is named rstudio.exe, but the file extension will typically be hidden, so look for rstudio. Right-click this executable to create a desktop shortcut. Double-click the executable or use the shortcut to open.

For all other operating systems

Download the relevant installer for your OS listed under “Installers for Supported Platforms”. Run the installer to complete installation.

Installing LaTeX (optional)

Installing LaTeX with a decent selection of packages is recommended, but takes some time - allow an hour for this step.

For Windows

Go to http://miktex.org/download and select Other Downloads. Select the Net Installer if you have 32-bit Windows or the 64-bit Net Installer if you have 64-bit Windows (If you are unsure whether you have 32 or 64 bit Windows, search for system in the Control Panel and look in the settings or system information). This installer allows you to download all packages and install a complete TeX/LaTeX system. Run the installer once to download the packages and then re-run to install. The install will select an appropriate location to install according to whether or not you have admin rights.

For Mac

Install MacTeX using the installer at http://www.tug.org/mactex/downloading.html.

For Linux

Install TeX Live for your distribution. Look up the options available in your package manager and select components to give a reasonably extensive/full installation. For example, the following packages are recommended for Ubuntu

  • texlive-latex-base
  • texlive-latex-extra
  • texlive-fonts-recommended

In addition, a package providing Texinfo and the Inconsolata font should be installed, e.g. on Ubuntu

  • texinfo
  • fonts-inconsolata

Development Tools (optional; never needed by most users)

For Windows with no admin rights

Download the latest Rtools installer, Rtools.exe, from https://cran.r-project.org/bin/windows/Rtools/. Run the installer making the following selections: keep the default settings for the installation location and components to install; keep the box to edit the system PATH unchecked and uncheck the box to save the version information to the registry. After the installation, go to the Windows Control Panel and search for env. Select Edit environment variables for your account. Under User variables for [username] click the New… button. In the Variable name box enter PATH and in the Variable value box enter C:\Rtools\bin;C:\Rtools\mingw-32\bin; then click OK to save the changes. Windows must be restarted for the system PATH to be updated, only then can R find the installed tools.

For Windows with admin rights

Download the latest Rtools installer, Rtools.exe, from https://cran.r-project.org/bin/windows/Rtools/. Run the installer making the following selections: keep the default settings for the installation location and components to install; check the box to edit the system PATH. Windows must be restarted for the system PATH to be updated, only then can R find the installed tools.

For Mac

Install XCode. Either:

  1. Download and install XCode from the Mac AppStore: http://itunes.apple.com/us/app/xcode/id497799835?mt=12
  2. Within XCode go to Preferences : Downloads and install the Command Line Tools

Or for a smaller download size:

  1. Register as an Apple Developer (free) here: https://developer.apple.com/programs/register/
  2. Download the Command Line Tools for XCode appropriate for the version of OS X you are running from here: https://developer.apple.com/downloads/

For Linux

If you installed r-base-dev, when installing R, you should have all you need to build packages from source. Otherwise return to the instructions for installing R for your distribution and follow the instructions there to install the additional tools.

Issues?

If you have problems installing R or RStudio on your laptop, then please post a question to the Vacation School Forum, or come to one of the setup clinic sessions during the week before the Vacation School. If you do not have a laptop with the required software installed you will need to use a lab computer instead, during the Vacation School lab time.