[Bioc-devel] Rendering of vignette R code on the website

Dan Tenenbaum dtenenba at fredhutch.org
Fri Jun 19 01:24:57 CEST 2015

----- Original Message -----
> From: "Wolfgang Huber" <whuber at embl.de>
> To: bioc-devel at r-project.org
> Sent: Thursday, June 18, 2015 5:47:27 AM
> Subject: [Bioc-devel] Rendering of vignette R code on the website
> Perhaps a buglet in the build system / the website code? --
> When I follow the link to “R Script” on the page
> http://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html
> (i.e.
> http://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.R
> ) the result is a nearly empty file.
> With other packages, e.g. BiocStyle, this does not happen, and code
> is shown:
> http://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle.R

I tracked this down and fixed it, results should be evident in the next build results (tomorrow late morning Seattle time).

> I am also confused about the first lines of both of these files:
> ### R code from vignette source
> 'vignettes/DESeq2/inst/doc/DESeq2.Rnw'
> ### R code from vignette source
> 'vignettes/BiocStyle/inst/doc/LatexStyle.Rnw'
> as the stated paths do (should) not exist.

They do exist on the machine where the Stangle/purl takes place, though I agree it's a bit confusing.
I will think about how to handle this.

Thanks for the report,

> Thanks and best wishes
> Wolfgang
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