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

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]]

        [[alternative HTML version deleted]]