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?
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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