Building a Bioconductor package using RStudio

Key resources

• Docker image: Docker Hub
• Workshop material: pkgdown website

Workshop description

This workshop gives an introductory overview of how to build a Bioconductor package.

Workshop participants will learn what makes a Bioconductor package special, how to get started building one and how to disseminate your final product. This workshop will feature introductory material, ‘live’ coding, and Q&A, all of which are adapted from the content below.

Instructor

• Saskia Freytag (saskia.freytag@perkins.uwa.edu.au)
• Peter Hickey (hickey@wehi.edu.au)

Pre-requisites

• Basic knowledge of R syntax.
• Github account!!!

Workshop Participation

Students will build a small package which is ideally version controlled. There will be a Q&A session in the second half of the workshop.

Workshop goals and objectives

Learning goals

• Understand the purpose of a package
• Learn about the essential building blocks of a package
• Develop your first simple package
• Become familiar with version control

Installation

This workshop uses Bioconductor version 3.12. At the time of writing, this is the current ‘devel’ version of Bioconductor, which can be installed following these instructions.

You can then install the packages necessary for this workshop using the following:

library(BiocManager)
install(c("usethis", "roxygen2", "devtools", "goodpractice", "BiocCheck"))

Alternatively, you can might like to use Docker to run the workshop in a container with R, all the necessary packages, and RStudio. This can be done as follows:

• Log in to RStudio at http://localhost:8787 using username rstudio and password welcome-to-bioc2020. Note that on Windows you need to provide your localhost IP address like http://191.163.92.108:8787/ - find it using docker-machine ip default in Docker’s terminal.
• Run browseVignettes(package = "Building a Bioconductor Package"). Click on one of the links, “HTML”, “source”, “R code”.
  • In case of The requested page was not found error, add help/ to the URL right after the hostname, e.g., http://localhost:8787/help/library/making_bioconductor_pkg/doc/Building_a_Bioconductor_Packages.html. This is a known bug.