[Bioc-devel] Fwd: Vignette warnings/errors

[Vincent Carey]

add something like this

vignette: >

  %\VignetteIndexEntry{[your index entry]}

  %\VignetteEngine{knitr::rmarkdown}

  %\VignetteEncoding{UTF-8}

to your vignette YAML ... see 1.4.2 of
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-package-vignettes

On Fri, May 11, 2018 at 1:47 PM, Kenneth Condon <roonysgalbi at gmail.com>
wrote:

> I forgot to add the YAML header of my .rmd file.
>
> ---
> title: "User Guide"
> author: "Kenneth Condon"
> date: "`r Sys.Date()`"
> output:
>     html_document:
>         number_sections: true
>         theme: cerulean
>         highlight: default
>         toc: TRUE
>         toc_depth: 3
>         toc_float:
>             collapsed: TRUE
>             smooth_scroll: FALSE
> ---
>
> Regards,
> Kenneth
>
> ---------- Forwarded message ----------
> From: Kenneth Condon <roonysgalbi at gmail.com>
> Date: Fri, May 11, 2018 at 6:37 PM
> Subject: Vignette warnings/errors
> To: bioc-devel <bioc-devel at r-project.org>
>
>
> Hi all,
>
> I'm hoping to submit my package soon. But I am having issues with the
> vignette.
>
> R CMD check results0 errors | 1 warning  | 0 noteschecking files in
> ‘vignettes’ ... WARNING
> Files in the 'vignettes' directory but no files in 'inst/doc':
>   ‘UserGuide.Rmd’, ‘UserGuide.html’, ‘images/benchmark.png’,
>     ‘images/workflow.png’
> Files named as vignettes but with no recognized vignette engine:
>    ‘vignettes/UserGuide.Rmd’
> (Is a VignetteBuilder field missing?)
>
>
> BiocCheck FAILED.$error
> [1] "VignetteBuilder listed in DESCRIPTION but not found as
> VignetteEngine in any vignettes:"
>
>
>
> My DESCRIPTION contains:
> RoxygenNote: 6.0.1
> Suggests: knitr,
>     rmarkdown,
>     testthat
> VignetteBuilder: knitr
>
> My directory tree looks as follows (note there is no inst/doc/ folder):
> data/
> man/
> R/
> tests/testthat/
> vignettes/images/
>
> Contents of vignettes/:
> images/benchmark.png
>
> images/workflow.png
>
> UserGuide.Rmd # created with use_vignette('UserGuide', pkg =
> myNewPackageName)
> Userguide.html # created successfully with knitr button in Rstudio
>
>
> Can someone instruct me what I am missing?
>
> Regards,
> Kenneth
>
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>
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