[Bioc-devel] BiocStyle issue

Yu, Guangchuang gcyu at connect.hku.hk
Wed Nov 23 03:46:54 CET 2016

Dear all,

I recompile my package and it throw the following error when building

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


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 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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