[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: "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.
> 

Not sure what you mean by that. I was able to build your package with no problem. You might try removing that symlink and installing pandoc with


sudo apt-get install pandoc

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
> > 
> 
>