Frederick Boehm
Frederick Boehm
Biostatistics, genetics, medicine, open science
Apr 1, 2018 2 min read

reticulate R package & Travis

I like to use Travis CI with my R packages. I recently wrote a R package, limmbo2, that is a wrapper for the python module limmbo. I used the R package reticulate, from Rstudio. I struggled for about 3 hours to write a .travis.yml file for limmbo2. Finally, I found a viable solution. I’m writing this blog post in hopes that it might be useful to myself and others in the future.

Why is using Travis CI potentially tricky for packages that use reticulate?

reticulate has python dependencies, so you have to ensure that any python modules that your package (or reticulate) uses are installed properly when Travis CI runs. Furthermore, the authors of the limmbo python module recommend that you use conda to install limmbo. This means that I needed to install conda on Travis CI. Fortunately, a web search turned up some useful yaml. I decided to set the python version variable to 2.7. I didn’t want to use python3, largely because I’ve really only worked with python2 in the past.

What is a solution to this?

Even though I haven’t yet written unit tests for limmbo2, I’m excited to have a .travis.yml file that results in a passing build on Travis CI.

Here is the .travis.yml file.

Caution

I need to caution readers that I haven’t verified that every line of my .travis.yml is needed. Rather, I just know that the current version yields a passing build.

If you have ideas for how I might improve the .travis.yml file, please write them in the comments, or submit a pull request.

Thanks!

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