Hi Richard,
It depends on the filetype. I am loading my "non RData" files with
read.delim and my RData files with a helper function which returns a R
object of the RData object:
#' Load RData object and returns first entry
#'
#' Load RData object and returns first entry. If there is more than one
#' object in the RData file, only the first object will be returned.
#'
#' @param RDataFile a \code{character} vector to the RData file.
#'
#' @return The \code{R} object of the RData file.
#' @export
#' @examples
#' # load GRanges object stored in a RData file.
#' dummy.GRanges <- loadRData(system.file('extdata', 'dummy.RData',
package = "dummyData"))
loadRData <- function(RDataFile) {
load(RDataFile)
objectToLoad <- ls()[ls() != "RDataFile"]
if (length(objectToLoad) > 1)
warning(paste0("RData file contains more than one object. Only the
first object (",
objectToLoad[1], ") will be returned!"))
get(objectToLoad[1])
}
I know this is not the best solution. I guess saving the R objects in
RDS files instead of RData files is the better solution here.
My question is if my storage of the RData objects (or RDS objects) in
the inst/extdata directory is ok for an Bioconductor package.
Best,
Tobias
Am 09.01.20 um 15:45 schrieb Richard Virgen-Slane:
>
> I may be missing a point, but how are you loading the saved files?
>
> On Thu, Jan 9, 2020 at 4:46 AM web working <webwork...@posteo.de
> <mailto:webwork...@posteo.de>> wrote:
>
> 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
> <http://r-pkgs.had.co.nz/data.html#other-data>). Is this the way
> how to do it?
>
> Best,
> Tobias
>
> _______________________________________________
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> list
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