[Bioc-devel] Package vignette and knitr

[davide risso]

Thank you Dan.

I should have looked at the time of my commit.

Best,
davide

On Tue, Apr 22, 2014 at 12:15 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>



-- 
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