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

[Leo Lahti]

Hi Dan, no problem with the code:
https://github.com/microbiome/microbiome/blob/master/vignettes/vignette.Rmd

Thanks ever so much for the support.

Leo



On Mon, Oct 6, 2014 at 4:59 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

>
>
> ----- Original Message -----
> > From: "Leo Lahti" <leo.lahti at iki.fi>
> > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > Cc: bioc-devel at r-project.org
> > Sent: Monday, October 6, 2014 7:55:07 AM
> > Subject: Re: [Bioc-devel] Fwd: Rmarkdown built html vignette not
> included in final package tarball
> >
> >
> >
> >
> > 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.
> >
>
>
> Can you post a link to your package code? If you'd prefer not to, you can
> send it to me off-list.
> Dan
>
> > 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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