[Bioc-devel] Fwd: Rmarkdown built html vignette not included in final package tarball

[Dan Tenenbaum]

----- Original Message -----
> From: "Leo Lahti" <leo.lahti at iki.fi>
> To: bioc-devel at r-project.org
> Sent: Monday, October 6, 2014 7:25:03 AM
> Subject: [Bioc-devel] Fwd: Rmarkdown built html vignette not included in final package tarball
> 
> Hi Sean, thanks again. Even this does not seem to help. The html file
> is
> not built from Rmd during package build.
> 

Do you have pandoc installed?
Dan


> If someone has pointers to functional examples I could try to compare
> and
> find the explanation.
> 
> best,
> Leo
> 
> On Mon, Oct 6, 2014 at 3:33 PM, Sean Davis <sdavis2 at mail.nih.gov>
> wrote:
> 
> >
> >
> > On Mon, Oct 6, 2014 at 9:25 AM, Leo Lahti <leo.lahti at iki.fi> wrote:
> >
> >> Thanks Sean, in fact I had already bumped into this very useful
> >> post.
> >>
> >> I tried to make the changes you suggested, yet the html file is
> >> not built
> >> as it should.
> >>
> >> Any pointers to public code for packages with successful automated
> >> builds
> >> of html vignettes from Rmd ?
> >>
> >> The current version of my package vignette is in:
> >>
> >> https://github.com/microbiome/microbiome/blob/master/vignettes/vignette.Rmd
> >> For some reason the html file fails to build during package build
> >> as it
> >> should.
> >>
> >>
> > Hi, Leo.
> >
> > This block:
> >
> > <!--
> >   %\VignetteEngine{knitr::rmarkdown}
> >   %\VignetteIndexEntry{microbiome tutorial}
> >   %\usepackage[utf8]{inputenc}
> > -->
> >
> > needs to go after the yaml header.
> >
> > Sean
> >
> >
> >
> >>
> >>
> >>
> >> On Mon, Oct 6, 2014 at 3:16 PM, Sean Davis <sdavis2 at mail.nih.gov>
> >> wrote:
> >>
> >> > Hi, Leo.
> >> >
> >> > I think you'll need to include the VignetteIndexEntry and
> >> > VignetteEngine
> >> > as the first lines of your vignette, enclosed in an HTML
> >> > comment.
> >> You'll
> >> > also need to adjust your DESCRIPTION file slightly.  Though not
> >> > meant
> >> to be
> >> > authoritative, I put together the details that worked for me
> >> > here:
> >> >
> >> >
> >> >
> >> http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/
> >> >
> >> > Sean
> >> >
> >> >
> >> > On Mon, Oct 6, 2014 at 8:23 AM, Leo Lahti <leo.lahti at iki.fi>
> >> > wrote:
> >> >
> >> >> Dear list,
> >> >>
> >> >> I have built html vignettes from Rmd files
> >> >>
> >> >> For this I have added the following lines in vignette start:
> >> >>
> >> >> ---
> >> >> title: "my vignette"
> >> >> author: "N.N"
> >> >> date: "`r Sys.Date()`"
> >> >> output: rmarkdown::html_vignette
> >> >> vignette: >
> >> >>   %\VignetteEngine{knitr::rmarkdown}
> >> >>   %\VignetteIndexEntry{my tutorial}
> >> >>   %\usepackage[utf8]{inputenc}
> >> >> ---
> >> >>
> >> >> and then run in R:
> >> >> rmarkdown::render("vignette.Rmd", "html_document")
> >> >>
> >> >> However after R CMD check and build, the html vignette is not
> >> >> included
> >> in
> >> >> the package tarball.
> >> >>
> >> >> How I can ensure that the html vignette will be included in the
> >> >> final
> >> >> tarball ? Querying the bioc list messages did not lead to
> >> >> solution so
> >> far.
> >> >>
> >> >>
> >> >> best regards
> >> >> Leo Lahti
> >> >>
> >> >>         [[alternative HTML version deleted]]
> >> >>
> >> >> _______________________________________________
> >> >> Bioc-devel at r-project.org mailing list
> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>
> >> >
> >> >
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 
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