[Bioc-devel] GitHub Pages Vignettes

[Shepherd, Lori]

This page is more accurate:

http://bioconductor.org/developers/package-guidelines/#vignettes

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:


diffexp.Rmd

pagoda.Rmd



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":

http://bioconductor.org/checkResults/release/bioc-LATEST/scde/malbec1-buildsrc.html

* 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
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
vignette: >
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteIndexEntry{BiocFileCache: Managing File Resources Across Sessions}
    %\VignetteEncoding{UTF-8}
    %\VignetteDepends{rtracklayer}
---

 Hope this helps.
Cheers,




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
Australia

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]