[Bioc-devel] BiocStyle issue

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
--
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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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