Author: Ildi Czeller, @czeildi on Twitter and Github
TL;DR
Save all datasets you refer to from your functions within an R package as internal data.
what I learned
In an R package you might have a dataset that you want to use in your functions and want to publicize as well as external dataset. In this case you should save this dataset as both internal and external data with
devtools::use_data(external_and_internal)
devtools::use_data(external_and_internal, internal = TRUE)
(More details in Hadley’s book on R packages.)
If you only save your data as external data:
You get a R CMD check note about undefined global variables: 'external_only'. This you can eliminate with
utils::globalVariables("external_only")
but then you only conceal the problem from yourself.
If your package is loaded, everything looks fine but if someone wants to use your function without loading your package:
datasetsexperiment::print_external_in_body()
it will fail with object 'external_only' not found. This error will be probably frustrating as your user can see the data just fine with
datasetsexperiment::external_only
I came across this scenario last week and I am really lucky that somehow I suspected that the dataset should be saved as internal data. Otherwise I honestly do not know how long would the debugging have been.
Previously I always loaded the package so it was strange to suddenly see it not working. Also running your testthat tests and devtools::load_all() both load external datasets so you won’t notice the problem during development.
detailed results
The exact scenario after devtools::install():
datasetsexperiment::print_internal_in_body()
#> [1] "piece of data saved as both internal and external"
datasetsexperiment::print_external_in_body()
#> Error in datasetsexperiment::print_external_in_body(): object 'external_only' not found
datasetsexperiment::external_only
#> [1] "piece of external only data"
library("datasetsexperiment")
datasetsexperiment::print_internal_in_body()
#> [1] "piece of data saved as both internal and external"
datasetsexperiment::print_external_in_body()
#> [1] "piece of external only data"
datasetsexperiment::external_only
#> [1] "piece of external only data"
remark
In the repository you can see an experiment where the used data is in a function argument or in the body. This is because I remember seeing one of them work and the other not but I could not reproduce this scenario.
material
Code (R code + Dockerfile) is available on GitHub.