[Bioc-devel] Package vignette and knitr

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