[R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation

[Ruff, Sergej]

So, in  the previous version of the package when we type ?bootGSEA, it opens the documentation in webpage (google, firefox…) and when we type ?pkg-function opens to the right side window, but now it just opens in the right side window. I was wondering why does it not open in webpage now.

________________________________
Von: Ruff, Sergej
Gesendet: Donnerstag, 7. März 2024 17:56:20
An: Hadley Wickham
Cc: r-package-devel using r-project.org
Betreff: AW: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r package documentation


the package is currently available under: https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r


line 1-31 contains the package information.


#' Package contains functions that repeates GSEA using bootstrap samples of gene sets. Bootstrap results are
#' aggregated to a new ranking score. The score can be compared to the gene set
#' ranking resulting from the standard GSEA.
#'
#' So far the functions included in the package are:
#' \itemize{
#'   \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
#'   \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate boostrap pathway analysis
#'   \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
#'   \item \code{\link{boot.GO}} Bootstrap GO analysis
#'   \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
#'   \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
#'   \item \code{\link{histDiff}} Visualization of difference in ranks
#'   \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
#' }
#'
#' \tabular{ll}{
#' Package: \tab bootGSEA\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0\cr
#' Date: \tab 2024-03-05\cr
#' License: \tab GPL (>= 3)\cr
#' }
#'
#' @author Shamini Hemandhar Kumar, Klaus Jung (\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
#'
#' Maintainer: Shamini Hemandhar Kumar (\email{shamini.hemandhar.kumar@@tiho-hannover.de})
#' @aliases bootGSEA
#' @title Robustness evaluation of gene set enrichment analysis (GSEA)
#' @keywords Robustness GSEA
"_PACKAGE"


________________________________
Von: Hadley Wickham <h.wickham using gmail.com>
Gesendet: Donnerstag, 7. März 2024 16:02:15
An: Ruff, Sergej
Cc: r-package-devel using r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r package documentation

Do you have a pointer to the roxygen2 comments that you're using?
Hadley

On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej <Sergej.Ruff using tiho-hannover.de<mailto:Sergej.Ruff using tiho-hannover.de>> wrote:
Hello,

I need help with a package I am currently developing called bootGSEA.
 I noticed that when I try ‘?bootGSEA’ it goes to the help page in R itself but not to the html page (we had this issue last time as well but we solved it by adding a documentation to the package itself to the R file) like from the before version of the package.
I tried “_PACKAGE” in the documentation of the package section as @doctype is depreceated, but it still doesn’t seem to solve the issue. Do you have any idea on this?


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