yes,
I am refering to Rstudio. I checked the settings and type is set to "htlm", not text. And I was wondering why the package documentation opened in a browser when I used @doctype. Maybe it has nothing to do with that but I can´t find the reason why it opened in the browser in the first place. ________________________________ Von: Jeff Newmiller <jdnew...@dcn.davis.ca.us> Gesendet: Donnerstag, 7. März 2024 20:57:58 An: r-package-devel@r-project.org; Ruff, Sergej; Hadley Wickham Cc: r-package-devel@r-project.org Betreff: [EXTERN] Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation What is a "right side window"? Are you mixing up what R does and what RStudio does? I think I agree with Ivan that this is a question about the environment in which you are loading the package rather than anything in the package itself. On March 7, 2024 11:21:06 AM PST, "Ruff, Sergej" <sergej.r...@tiho-hannover.de> wrote: >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 -- Sent from my phone. Please excuse my brevity. [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel