[Bioc-devel] Fwd: Vignette warnings/errors

[Kenneth Condon]

Such a simple fix, thank you Vincent.

On Fri, May 11, 2018 at 7:11 PM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> 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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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