[Bioc-devel] GitHub Pages Vignettes

[Dario Strbenac]

Good day,

On the Bioconductor website, scde has no vignettes listed in the Documentation section. Looking at the contents of the package, there is a vignettes directory with four vignettes in it. They each have output: md_document and are hosted on GitHub.io. The vignettes also are not accessible from within R

> browseVignettes("scde")
No vignettes found by browseVignettes("scde")

Is such a documentation design choice suitable for Bioconductor packages? The Vignettes section of Package Guidelines states that a vignette is mandatory, but there is no statement about acceptable output formats of vignettes. Also, the Package Vignettes webpage seems to have been written before HTML vignettes were possible, because it refers only to Rnw and PDF files. Its URL is http://bioconductor.org/help/package-vignettes/ Could such requirements be made explicit?

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia