Walter and Eliza Hall Institute

September 16, 2019

09:00 - 17:00

Instructors: Luke Zappia

Helpers: Ilariya Tarasova, Harry Wang

General Information

COMBINE is an Australian organisation for students in computational biology, bioinformatics, and related fields. COMBINE is the student subcommittee of the Australian Bioinformatics And Computational Biology Society (ABACBS) as well as the official International Society for Computational Biology (ISCB) Regional Student Group (RSG) for Australia. We aim to bring together students and early-career researchers from the computational and life sciences for networking, collaboration, and professional development.

This workshop teaches the basics of developing an R package. By the end of the workshop you should have built your own personal R package to hold functions you commonly use. More details about the workshop content are provided in the Syllabus section below.

We have tried to keep the cost of the workshop as low as possible with the help of our generous sponsors. The registration fee helps us to cover the cost of morning tea, lunch and afternoon tea which will be provided on the day. Discounted registration is available for students and ABACBS members. An ABACBS student membership is only $20 and comes with other benefits including discounted registration for the annual COMBINE symposium. More information about ABACBS membership can be found on the ABACBS website.

Who: This workshop is aimed at researchers who are comfortable with R but want to learn how to develop their own packages. It assumes you are familiar with using R and RStudio.

Where: 1G, Royal Parade, Parkville VIC 3052. Get directions with OpenStreetMap or Google Maps.

When: September 16, 2019. Add to your Google Calendar.

Registrations: Register on the ABACBS website.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop. If you have any other needs please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.


WEHI logo


Day 1

Before Follow setup instructions
09:00 Registration and help setting up
09:30 Introduction
10:00 Creating a package
10:30 Morning tea
11:00 Functions and documentation
12:30 Lunch break
13:00 Testing
14:00 Dependencies
15:00 Afternoon tea
15:30 Building and releasing
16:30 Wrap-up


R package development

The materials for this workshop are available here. Some of the topics included in the workshop are:

  • Setting up a package
  • Adding functions
  • Running package checks
  • Documentation
  • Testing
  • Dependencies
  • Releasing a package


To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

A list of common issues that occur during installation can be found on the Software Carpentry Configuration Problems and Solutions wiki page.

R and RStudio

You will need a relatively recent version of R installed. We will also be using RStudio for the workshop so make sure that is installed and up to date.

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

Git and GitHub

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on You will need a supported web browser.

We will not be teaching Git in this workshop but we will show you how to upload your package to GitHub using R. To participate in this part of the workshop. You will need an account at Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git for windows can be downloaded from here.

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.