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@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.wick...@gmail.com> Gesendet: Donnerstag, 7. März 2024 16:02:15 An: Ruff, Sergej Cc: r-package-devel@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.r...@tiho-hannover.de<mailto:sergej.r...@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? [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel -- http://hadley.nz [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
