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

[Ruff, Sergej]

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 <jdnewmil using dcn.davis.ca.us>
Gesendet: Donnerstag, 7. März 2024 20:57:58
An: r-package-devel using r-project.org; Ruff, Sergej; Hadley Wickham
Cc: r-package-devel using 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.Ruff using 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 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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>
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>
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>
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--
Sent from my phone. Please excuse my brevity.

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