[Bioc-devel] BiocStyle issue

[Leonardo Collado Torres]

Guangchuang, you can see at
https://github.com/Bioconductor/BiocStyle/issues/19 (the main github
repo for this package) that this issue is already been reported and
will be addressed asap by BiocStyle's maintainer.

On Tue, Nov 22, 2016 at 9:46 PM, Yu, Guangchuang <gcyu at connect.hku.hk> wrote:
>
> Dear all,
>
> I recompile my package and it throw the following error when building
> vignettes:
>
> unused arguments (self_contained, lib_dir, output_dir)
>
> I search  ?opts_knit, and couldn't find these parameters.
>
> In ?opts_knit, I find *self.contained* instead of *self_contained*.
>
> I remove the dependency of BiocStyle and recompile my package and it works.
>
>
> I search the source code of BiocStyle, and find the issue in
>
> https://github.com/Bioconductor-mirror/BiocStyle/blob/master/R/html_document.R#L66-L70
>
> Now rmarkdown:::pandoc_html_highlight_args (in latest release version 1.2)
> only accepts template and highlight parameters.
>
> This will fail the compilation of many Bioconductor packages. Please fix it.
>
> Using ::: is not recommended by Bioconductor and will not passed by
> BiocCheck (if I remember it correctly). But I find several packages by
> Bioconductor core team use it.
>
> Best wishes,
> Guangchuang
> --
> --~--~---------~--~----~------------~-------~--~----~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~----------~----~----~----~------~----~------~--~---
>
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>
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