[Bioc-devel] Package vignette and knitr

[Dan Tenenbaum]

Hi Davide,

----- Original Message -----
> From: "davide risso" <risso.davide at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Tuesday, April 22, 2014 12:06:09 PM
> Subject: [Bioc-devel] Package vignette and knitr
> 
> Dear list,
> 
> I've modified the vignette of my EDASeq package to work with knitr.
> 
> Following the guidelines in the BiocStyle vignette, I've added
> 
> Suggests: BiocStyle, knitr
> VignetteBuilder: knitr
> 
> to the DESCRIPTION file and
> 
> %\VignetteEngine{knitr::knitr}
> 
> to the top of the .Rnw file.
> 
> The package builds fine on my machine, but does not build in any of
> the Bioconductor machines:
> http://master.bioconductor.org/checkResults/devel/bioc-LATEST/EDASeq/zin1-buildsrc.html
> 
> Command output
> * checking for file ‘EDASeq/DESCRIPTION’ ... OK
> * preparing ‘EDASeq’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> Quitting from lines 67-69 (EDASeq.Rnw)
> Error: processing vignette 'EDASeq.Rnw' failed with diagnostics:
> object 'opts_chunk' not found
> Execution halted
> 
> Lines 67-69 are:
> 
> <<setup, echo=FALSE>>=
> library(knitr)
> opts_chunk$set(dev="pdf", fig.align="center", cache=FALSE,
> message=FALSE, out.width=".55\\textwidth", echo=TRUE,
> results="markup", fig.show="hold")
> options(width=60)
> @
> 
> Am I missing something?
> 

You added the line 
library(knitr)

after 5PM yesterday (Seattle time) too late to make it into today's build report. It should be OK tomorrow.

Dan



> Best,
> davide
> 
> --
> Davide Risso, PhD
> Post Doctoral Scholar
> Department of Statistics
> University of California, Berkeley
> 344 Li Ka Shing Center, #3370
> Berkeley, CA 94720-3370
> E-mail: davide.risso at berkeley.edu
> 
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