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

[Leo Lahti]

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.





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

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