Articles by Colin Gillespie

Detecting Security Vulnerabilities in R Packages

August 28, 2020 | Colin Gillespie

One of our main roles at Jumping Rivers is to set-up and provide ongoing maintenance to R, Python and RStudio infrastructure. This typically involves ensuring software is up-to-date and making sure everything is running smoothly. The OSS Index developed by Sonatype is a free catalogue of open source components and ... [Read more...]

Speeding up your Continuous Integration Builds

June 25, 2020 | Colin Gillespie

Continuous integration is an amazing tool when developing R packages. We push a change to the server, and a process is spawned that checks we haven’t done something silly. It protects us from ourselves! However this process can become slow, as typically the CI process starts with a blank ... [Read more...]

Setting the Graphics Device in a RMarkdown Document

April 15, 2020 | Colin Gillespie

In our recent post about saving R graphics, it became obvious that achieving consistent graphics across platforms or even saving the “correct” graph on a particular OS was challenging. Getting consistent fonts across platforms often failed, and for the default PNG device under Windows, anti-aliasing was also an issue. The ...

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Saving R Graphics across OSs

April 13, 2020 | Colin Gillespie

R is known for it’s amazing graphics. Not only ggplot2, but also plotly, and the other dozens of packages at the graphics task view. There seems to be a graph for every scenario. However once you’ve created your figure, how do you export it? This post compares standard ...

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Faster R package installation

March 23, 2020 | Colin Gillespie

Faster package installation Every few weeks or so, a tweet pops up asking about how to speed up package installation in R Depending on the luck of twitter, the author may get a few suggestions. The bigger picture is that package installation time is starting to become more of an ...

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Customising your Rprofile

January 17, 2020 | Colin Gillespie

What is an Rprofile Every time R starts, it runs through a couple of R scripts. One of these scripts is the .Rprofile. This allows users to customise their particular set-up. However, some care has to be taken, as if this script is broken, this can cause R to break. ...

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Job: Junior Systems Administrator (with a focus on R/Python)

October 17, 2019 | Colin Gillespie

Jumping Rivers is a data science consultancy company focused on R and Python. We work across industries and throughout the world. We offer a mixture of training, modelling, and infrastructure support. Jumping Rivers is an RStudio Full Service Certified Partner. This role is suitable for anyone interested in deploying (Linux-based) ... [Read more...]

Timing hash functions with the bench package

May 21, 2019 | Colin Gillespie

This blog post has two goals Investigate the bench package for timing R functions Consequently explore the different algorithms in the digest package using bench What is digest? The digest package provides a hash function to summarise R objects. Standard hashes are available, such as md5, crc32, sha-1, and sha-256. ...

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benchmarkme: new version

January 29, 2019 | Colin Gillespie

When discussing how to speed up slow R code, my first question is what is your computer spec? It’s always surprised me that people are wondering why analysing big data is slow, yet they are using a five-year-old cheap laptop. Spending a few thousand pounds would often make their ...

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Hacking Bioconductor

November 19, 2018 | Colin Gillespie

Introduction Domain squatting or URL hijacking is a straightforward attack that requires little skill. An attacker registers a domain that is similar to the target domain and hopes that a user accidentally visits the site. For example, if the domain is example.com, then a typo-squatter would register similar domains ...

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What R version do you really need for a package?

November 1, 2018 | Colin Gillespie

At Jumping Rivers we run a lot of R courses. Some of our most popular courses revolve around the tidyverse, in particular, our Introduction to the tidyverse and our more advanced mastering course. We even trained over 200 data scientists NHS – see our case study for more details. As you can ...

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R from the turn of the century

September 20, 2018 | Colin Gillespie

Last week I spent some time reminiscing about my PhD and looking through some old R code. This trip down memory lane led to some of my old R scripts that amazingly still run. My R scripts were fairly simple and just created a few graphs. However now that I’...