Hi Davide,
----- Original Message -----
> From: "davide risso" <risso.dav...@gmail.com>
> To: bioc-devel@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.ri...@berkeley.edu
>
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