[Bioc-devel] Package Without a Vignette

[Dan Tenenbaum]

The nightly builds run every night (except Friday night) and if your commits are done before 5:20 PM (Seattle time) they will be reflected in the next day's build report.

But you don't need the build system or even travis to see if your vignette will be built by R CMD build.

All you have to do is run "R CMD build cogena" and if you see the line

* installing the package to build vignettes

then it means your vignettes will be created. If you don't see that line, the vignettes will not be built.

Dan




----- Original Message -----
> From: "Zhilong Jia" <zhilongjia at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Saturday, April 2, 2016 7:23:14 PM
> Subject: Re: [Bioc-devel] Package Without a Vignette

> Hi Dan,
> 
> Thank you. I updated it.
> 
> At the beginning,  knitr was used but would result in errors in travis-ci,
> like https://github.com/ropensci/rentrez/issues/71 and
> https://github.com/ropensci/rentrez/commit/8ee84ba29472f56f3f92bf65511e1a29121882d4
> so I changed knitr into rmarkdown and it works in travis-ci. I'm not sure
> what's the problem here exactly? Thank you.
> 
> For cogena's travis-ci
> 
> the knitr one is : https://travis-ci.org/zhilongjia/cogena/builds/119812514
> the rmarkdown one is:
> https://travis-ci.org/zhilongjia/cogena/builds/119819020
> 
> BTW, it seems there is a 2-3 days delay for  bioconductor to build the
> updated package. Is there a way for users to build it immediately by
> themselves?
> 
> Cheers,
> Zhilong
> 
> 
> On 3 April 2016 at 09:09, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> 
>> 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
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>> >> > >
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>> >
>> >
>> >
>> > --
>> > Zhilong JIA
>> > zhilongjia at gmail.com
>> > https://github.com/zhilongjia
>> >
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> 
> 
> 
> --
> Zhilong JIA
> zhilongjia at gmail.com
> https://github.com/zhilongjia