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?