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

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.

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

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