Hi all, I am trying to format my data.R file in an ExperimentHub package but have ran into issues when running checks. Note that my data package has a load function; zzz.r, so datasets can be called as such dataset_name(). An example of one dataset in my data.R file is
``` #' All MGI gene symbols with ENSEMBL gene IDs #' #' A dataset containing all MGI symbols in first column, then ensembl_gene_id #' in second column #' #' @source #' The code to prepare the .Rda file file from the marker file is: #' \code{ #' listMarts(host="www.ensembl.org") #' mouse <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", #' dataset="mmusculus_gene_ensembl") #' all_mgi_wtEnsembl = getBM(attributes=c("mgi_symbol","ensembl_gene_id"), #' mart=mouse) #' save(all_mgi_wtEnsembl,file="all_mgi_wtEnsembl.Rda") #' } #' @usage all_mgi_wtEnsembl(metadata=FALSE) #' @aliases all_mgi_wtEnsembl #' @examples all_mgi_wtEnsembl <- ewceData::all_mgi_wtEnsembl() #' "all_mgi_wtEnsembl" ``` The package works fine but my issue is regarding the use of the usage, aliase and example roxygen arguments above. Currently, I get the error from CRAN checks: ``` Undocumented arguments in documentation object 'all_mgi_wtEnsembl' �metadata� Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter �Writing R documentation files� in the �Writing R Extensions� manual. ``` Does anyone know what way the data.R file should be formatted to avoid issues? Kind regards, Alan. Alan Murphy Bioinformatician Neurogenomics lab UK Dementia Research Institute Imperial College London [[alternative HTML version deleted]]
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