[Bioc-devel] Formatting of ExperimentHub Data in package

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Feb 26 17:53:07 CET 2021

I think because you specified:
#' @usage all_mgi_wtEnsembl(metadata=FALSE)

You would need to document the parameter metadata with:
#' @param metadata <description of metadata object>


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Murphy, Alan E <a.murphy using imperial.ac.uk>
Sent: Friday, February 26, 2021 7:26 AM
To: bioc-devel <bioc-devel using r-project.org>
Subject: [Bioc-devel] Formatting of ExperimentHub Data in package

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="http://secure-web.cisco.com/1KPTRVfVjgi1pGO653PgYgUHtoJV_h-fKAGjmQzQO00OCDw8Rsqj0hm7EuhJ_KGfuDU_3Fu4mXRHR6DSUCdh2tVXmKNBT-VsybiMn7lSwHqmpWGanoJPnR3DZDpQIqstbW5vyYfbrYqCdazAcF-57ifCyj6qb5_YpeefYBZ5XOGKjFawZA5shw7jD0LYKxNkoUwX5ln24poiCK5hVLx6qcgpel1EDwWtTbi9mlDvGFrEoeQZHBNnSX7Zjm0FhEpWGm-aPNMWNX_nddKn4pjbflqzEDkZlWIiilK0RQyB9vaTSYfPG_ycq8St63c3uwVPL/http%3A%2F%2Fwww.ensembl.org")
#' mouse <- useMart(host="http://secure-web.cisco.com/1KPTRVfVjgi1pGO653PgYgUHtoJV_h-fKAGjmQzQO00OCDw8Rsqj0hm7EuhJ_KGfuDU_3Fu4mXRHR6DSUCdh2tVXmKNBT-VsybiMn7lSwHqmpWGanoJPnR3DZDpQIqstbW5vyYfbrYqCdazAcF-57ifCyj6qb5_YpeefYBZ5XOGKjFawZA5shw7jD0LYKxNkoUwX5ln24poiCK5hVLx6qcgpel1EDwWtTbi9mlDvGFrEoeQZHBNnSX7Zjm0FhEpWGm-aPNMWNX_nddKn4pjbflqzEDkZlWIiilK0RQyB9vaTSYfPG_ycq8St63c3uwVPL/http%3A%2F%2Fwww.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()

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 Murphy
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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