[Bioc-devel] BiocStyle issue

[Yu, Guangchuang]

I found the issue was filed by yihui half month ago on github,
https://github.com/Bioconductor/BiocStyle/issues/18, and the solution is
quite intuitive by removing those un-supported paramters (self_contained,
lib_dir, output_dir). Hope it will be fixed soon.


On Wed, Nov 23, 2016 at 2:25 PM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

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



-- 
--~--~---------~--~----~------------~-------~--~----~
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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