[Bioc-devel] Package Without a Vignette

Sun Apr 3 08:51:24 CEST 2016

Hi Dan,

*R CMD build cogena (first try):*

* checking for file ‘cogena/DESCRIPTION’ ... OK
* preparing ‘cogena’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please
install both.
Error: processing vignette 'cogena-vignette_html.Rmd' failed with
diagnostics:
It seems you should call rmarkdown::render() instead of knitr::knit2html()
because cogena-vignette_html.Rmd appears to be an R Markdown v2 document.
Execution halted

*R CMD build cogena (after installing pandoc, pandoc-citeproc and nothing
changes of code):*

* checking for file ‘cogena/DESCRIPTION’ ... OK
* preparing ‘cogena’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘cogena_1.5.3.tar.gz’

So it means the vignette will be fine in the Bioconductor website?

About the "It seems you should call rmarkdown::render() instead of
knitr::knit2html() because cogena-vignette_html.Rmd appears to be an R
Markdown v2 document.", which also appears in the travis-ci, it seems travis-ci
did not install the pandoc, pandoc-citeproc, resulting in this issue.

Regards,
Zhiong

On 3 April 2016 at 11:51, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:

> 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
> >> >> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >> > >
> >> >> >
> >> >> >
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> >> >>         [[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
>

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

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