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

[Leo Lahti]

Hi Sean, thanks again. Even this does not seem to help. The html file is
not built from Rmd during package build.

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
>>
>
>

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