[Bioc-devel] GitHub Pages Vignettes

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Fri Mar 15 13:08:56 CET 2019

This page is more accurate:


but we should update the /help/package-vignettes/  as well thank you for pointing to this.

Keep in mind that the github repo is not the canonical location for Bioconductor package.  On Bioconductor I only see 2 Rmd vignettes in the directory.  The maintainers should probably sync their github repo with Bioconductor for all these vignettes to appear.  The only two files we see on the Bioconductor git server are:



In order to be accessible on the package landing page the vignettes must be rebuild and have the regenerated output processed.  If the pages are not rebuild then they will not appear on the landing page or be accessible in R.

>From the build report it seems to be the case that it skips the building of the vignette as there is no line  "* creating vignettes ... OK":


* checking for file �scde/DESCRIPTION� ... OK
* preparing �scde�:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a �data/datalist� file should be added
* building �scde_2.10.1.tar.gz�

Looking at the vignettes.  The header is missing the needed vignette metadata specifications for R to recognize these files.

The head of the diffexp.Rmd:

title: "Getting Started with `scde`"
author: "Peter Kharchenko, Jean Fan"
date: '`r Sys.Date()`'
output: pdf_document

Vignettes need to be specified with designation (example from BiocFileCache vignette):

title: "BiocFileCache: Managing File Resources Across Sessions"
author: Lori Shepherd
    toc: true
    toc_depth: 2
vignette: >
    %\VignetteIndexEntry{BiocFileCache: Managing File Resources Across Sessions}

 Hope this helps.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Dario Strbenac <dstr7320 using uni.sydney.edu.au>
Sent: Thursday, March 14, 2019 2:00:07 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] GitHub Pages Vignettes

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?

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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