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

[Leo Lahti]

Hi Dan,

The command "pandoc -v" gives: "pandoc 1.12.4.2" so the version seems to be
ok. I am also able to convert md file to html in R with the knitr::pandoc
command so pandoc seems to work.

However it might be worth noting that I am using pandoc via a symbolic link
from RStudio binaries
/usr/lib/rstudio/bin/pandoc/pandoc since updating to pandoc >=1.12.3
otherwise in Ubuntu 14.04 has appeared quite problematic.

Leo



On Mon, Oct 6, 2014 at 4:35 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

>
>
> ----- 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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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