R is a great tool for analysing data with an intuitive and interactive programming language. There are a number of limitations with an interactive programming language compared to compiled languages, such as higher memory and processing requirements. One way of overcoming these requirements is to use cloud computing, such as Amazon EC2. The Bioconductor group has an Amazon Machine Image with the latest version of R and RStudio; however, there is a major security hole in the default setup that allows others to “borrow” the resources you are paying for as well as being able to steal your data. This post highlights how to close this hole and securely use R and RStudio on Amazon EC2.