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.
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:
- The room is wheelchair / scooter accessible.
- Accessible restrooms are available.
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 combine@combine.org.au for more information.
Sponsors
Schedule
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 |
Syllabus
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
Setup
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.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
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 github.com. 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 github.com. 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.
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.