[Bioc-devel] Package Without a Vignette

[Zhilong Jia]

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
> >> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> > >
> >> >
> >> >
> >> > This email message may contain legally privileged and/or confidential
> >> > information.  If you are not the intended recipient(s), or the
> employee
> >> or
> >> > agent responsible for the delivery of this message to the intended
> >> > recipient(s), you are hereby notified that any disclosure, copying,
> >> > distribution, or use of this email message is prohibited.  If you have
> >> > received this message in error, please notify the sender immediately
> by
> >> > e-mail and delete this email message from your computer. Thank you.
> >> >
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> >
> > --
> > Zhilong JIA
> > zhilongjia at gmail.com
> > https://github.com/zhilongjia
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Zhilong JIA
zhilongjia at gmail.com
https://github.com/zhilongjia

	[[alternative HTML version deleted]]