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date: 2017-05-17T22:00:15Z
title: "Using travis-ci in research compendia and student repos"
In general I'm a big believer in the R package mechanism as a convenient way to package and distribute a reproducible compendium of code, data, notebooks and manuscripts. However, it's often overkill, particularly since passing basic continuous integration checks (e.g. via `devtools::use_travis()`) means running a relatively strict `R CMD check` that will worry about things such as documentation norms and details that aren't always appropriate.
What I most want is an easy way to confirm that any `.Rmd` notebooks in a repository can be successfully knit on an independent machine -- i.e. that the compendium can access all the software / functions and data it needs. Sure, some additional checks might be necessary (though these are sometimes best formulated in possibly-hidden `.Rmd` chunks), but this would detect the main ills such as failing to load libraries or using user-specific absolute paths.
A light-weight solution proposed in [this ropensci thread]( inspired me to write this [mock-up compendium]( which does just that, using a DESCRIPTION file to indicate dependencies and other metadata, and a `test.R` script called by `.travis.yml` to `rmarkdown::render` all the `.Rmds`:
Package: compendium
Version: 0.1.0
Depends: tidyverse, rmarkdown
A Package name and version are required for `devtools::install()` to work. Hopefully this approach also helps transition users towards providing more metadata in DESCRIPTION files, such as Author, author role, and License information.
Here's my `test.R` script:
f <- list.files(recursive = TRUE)
Rmds <- f[grepl(".Rmd$", f)]
lapply(Rmds, rmarkdown::render)
though one could clearly imagine permutations on this. (The thread discusses supporting `make`, or using a particular directory structure to decide what does and doesn't get run.)
Getting this to exploit `r-travis` (which does a nice job of handling key things like installing and caching installs of packages) involves just a minor tweak to providing a different `script:` testing routine from the default of `R CMD build`, `R CMD INSTALL` and `R CMD CHECK`:
language: R
sudo: false
cache: packages
- R -e "devtools::install()"
- R -f test.R
We'll see how this goes in practice.