When using `BiocStyle` with `pkgdown: as_is` I get error: Error in `haystack[haystack$similar > 0, ]`:

[Rohit-Satyam]

I have some Vignettes written using good practices of the BiocStyle format that I wanted to convert to a pkgdown website. However, I can't replace BiocStyle::html_document: with bookdown::html_document2 because then the bookdown then start complaining about places where I used BiocStyle functions, such as where Rpackage is BiocStyle function.

The `r Rpackage("testpkg")` has been developed .....

When using pkgdown: as_is: true followed by running build_site(devel=TRUE), I get the following error:

Reading vignettes/Gene_ID_Conversion.Rmd
Error in `haystack[haystack$similar > 0, ]`:
! incorrect number of dimensions
Run `rlang::last_trace()` to see where the error occurred.

output: 
  BiocStyle::html_document:
    toc_float: true
    toc: true
    number_sections: true
pkgdown:
  as_is: true

[Rohit-Satyam]

Also, unlike BiocStyle, where I can easily link my markdown tables using \@ref(tab:table1) and : (#tab:table1) List of search functions available in testpkg, pkgdown renders these lines as normal text. Is there an easy workaround so that I don't have to maintain separate copy of the vignettes for pkgdown website?

[Rohit-Satyam]

In addition, I am trying to change the tab names from "Articles" to "Vignettes" and "Reference" to "Functions"

I tried the following but this replaced the dropdown menu too

navbar:
  structure:
    left:
      - home
      - reference
      - articles
      - news
  components:
    articles:
      text: "Vignettes"

[jayhesselberth]

I'm not aware of an easy workaround for your vignette issues.

You might try migrating to a quarto vignette and forego the as_is approach. If you called library(BiocStyle) in the vignette then I guess you'd have access to its exported functions.

Regarding the navbar customization, I think you'd then need to list the vignettes you want to see to maintain the dropdown.