[Bioc-devel] No vignette contents page/fig refs with Devtools build

[Dan Tenenbaum]

----- Original Message -----
> From: "Steven Barrett" <Steven.J.Barrett at gsk.com>
> To: bioc-devel at r-project.org
> Sent: Monday, March 16, 2015 8:54:58 AM
> Subject: [Bioc-devel] No vignette contents page/fig refs with Devtools build
> 
> Hello,
> 
> I have a problem with the automated vignette construction during a
> devtools build.

I don't know what you mean by a devtools build; are you talking about the automated build that occurs when you submit a package to Bioconductor? If so, what is the name of the package? If you have not submitted the package to Bioconductor, maybe you can explain exactly what command you are using to build it. And perhaps you can send me (off list) the package.

Dan


> 
> The vignette is encoded in an .rnw file and I'm using Knitr.
> 
> When I compile the .rnw in RStudio it yields a .pdf with the contents
> page and figure label references properly instantiated.
> 
> However, when I include the .rnw in the package I'm building via
> devtools build the .pdf vignette is produced without the contents
> page and figure label references properly instantiated.
> 
> The package builds fine otherwise and there are no problems reported
> by devtools check or  Biocheck.
> 
> I would be most grateful for any suggestions as to what might be the
> issue.
> 
> Thanks,
> 
> Steven
> 
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