[Bioc-devel] How to use RData files in Bioconductor data and software packages

web working webwork|ng @end|ng |rom po@teo@de
Thu Jan 9 13:45:43 CET 2020

Dear all,

I am currently developing a software package (dummySoftware) and a data package (dummyData) and I am a bit confused in where to store my RData files in the data package. Here my situation:

I want to store some software package objects (new class objects of the software package) in the data package. This objects are example objects and a to big for software packages. As I have read here (http://r-pkgs.had.co.nz/data.html) all RData objects should be stored in the data directory of a package. BED files of the data package are stored in inst/extdata.
The data of the data packaged will be addressed in the software package like this: system.file('extdata', 'subset.bed', package = 'dummyData'). And here the problem occurs. After building the data package (devtools::build(args = c('--resave-data'))), all data in data/ are stored in a datalist, Rdata.rdb, Rdata.rds and Rdata.rdx and can not addressed with system.file. Addressing this data with the data() function results in a warning during BiocCheck::BiocCheck().

My solution is to store the RData files in the inst/extdata directory and address them with system.file. Something similar is mentioned here, but in the context of a vignette (r-pkgs.had.co.nz/data.html#other-data). Is this the way how to do it?


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