[Bioc-devel] Package Without a Vignette

[Dan Tenenbaum]

In DESCRIPTION change 

VignetteBuilder: rmarkdown

to 

VignetteBuilder: knitr

Dan


----- Original Message -----
> From: "Zhilong Jia" <zhilongjia at gmail.com>
> To: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Saturday, April 2, 2016 5:48:59 PM
> Subject: Re: [Bioc-devel] Package Without a Vignette

> Hi,
> 
> I just found no vignette for my updated package cogena
> <http://bioconductor.org/packages/3.3/bioc/html/cogena.html> (1.5.2),
> though there are vignettes  in the code. And the check CMD is
> /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
> cogena_1.5.2.tar.gz in
> http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html
> 
> And the similar section is here:
> 
> vignette: >
>  %\VignetteIndexEntry{Vignette Title}
>  %\VignetteEngine{knitr::rmarkdown}
>  %\usepackage[utf8]{inputenc}
> 
> No \\ here.
> 
> 
> Thank you.
> 
> Regards,
> Zhilong
> 
> 
> On 22 March 2016 at 18:24, Stefan Haunsberger <stefan.haunsberger at gmail.com>
> wrote:
> 
>> Hi,
>>
>> Yes, my bad. I'm already on it.
>>
>> Thanks,
>> Stefan
>>
>> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
>> martin.morgan at roswellpark.org> wrote:
>>
>> >
>> >
>> > On 03/22/2016 03:00 AM, Dario Strbenac wrote:
>> > > Hello,
>> > >
>> > > The newly added Bioconductor package miRNAmeConverter has no vignette,
>> > although a vignette is a requirement for Bioconductor packages which are
>> > not simply annotation databases.
>> >
>> > Rather, the package has a vignette, but it is not built.
>> >
>> > This is because of the '\\' in the vignette header. Also, the 'html' and
>> > 'pdf' versions of the vignette should not be in SVN.
>> >
>> > I've cc'd the maintainer.
>> >
>> > Martin
>> >
>> >
>> > Index: miRNAmeConverter-vignette.Rmd
>> > ===================================================================
>> > --- miRNAmeConverter-vignette.Rmd       (revision 115094)
>> > +++ miRNAmeConverter-vignette.Rmd       (working copy)
>> > @@ -9,9 +9,9 @@
>> >   csl: apa.csl
>> >   bibliography: references.bib
>> >   vignette: >
>> > -   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
>> > -   %\\VignetteEncoding{UTF-8}
>> > -   %\\VignetteEngine{knitr::rmarkdown}
>> > +   %\VignetteIndexEntry{miRNAmeConverter-vignette}
>> > +   %\VignetteEncoding{UTF-8}
>> > +   %\VignetteEngine{knitr::rmarkdown}
>> >   ---
>> >
>> >   <!-- output:
>> >
>> >
>> > >
>> > > --------------------------------------
>> > > Dario Strbenac
>> > > PhD Student
>> > > University of Sydney
>> > > Camperdown NSW 2050
>> > > Australia
>> > > _______________________________________________
>> > > Bioc-devel at r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
>> >
>> >
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>>
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> 
> 
> 
> --
> Zhilong JIA
> zhilongjia at gmail.com
> https://github.com/zhilongjia
> 
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> 
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