I'm trying to document some datasets in an R package using roxygen2. Considering just one of these:
- I have
mypkg/data/CpG.human.GRCh37.RDa - which contains an object called
CpG.human.GRCh37 and a file called:
mypkg/R/cpg-data.R, which contains:#' @name CpG.human.GRCh37 #' @title CpG islands - human - genome build: GRCh37/hg19 #' @description This data set list the genomic locations of human CpG islands, #' with coordinates based on the GRCh37 / hg19 genome build. #' @docType data #' @usage CpG.human.GRCh37 #' @format a \code{RangedData} instance, 1 row per CpG island. #' @source UCSC Table Browser #' @author Mark Cowley, 2012-03-05 #' @export NULL
When I roxygenize, this gets created mypkg/man/CpG.human.GRCh37.Rd, containing:
\docType{data}
\name{CpG.human.GRCh37}
\alias{CpG.human.GRCh37}
\title{CpG islands - human - genome build: GRCh37/hg19}
\format{a \code{RangedData} instance, 1 row per CpG island.}
\source{
UCSC Table Browser
}
\description{
This data set list the genomic locations of human CpG
islands, with coordinates based on the GRCh37 / hg19
genome build.
}
\author{
Mark Cowley, 2012-03-05
}
\usage{CpG.human.GRCh37}
\keyword{datasets}
and export(CpG.human.GRCh37) gets added the NAMESPACE file.
but when I R CMD CHECK I get:
...
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) :
undefined exports: CpG.human.GRCh37
Error: loading failed
...
Nowhere have I told R where to find this dataset, though I would assume that the mypkg/data/<name>.RDa would be a good first guess.
Any hints would be awesome.
If Hadley's watching, I notice that an \usage section is not created and the @usage directive is ignored.
i'm using roxygen-2.2.2, on R 2.13.1
@exportdirective is used for data sets. Try removing this. – Titular