[Bioc-devel] BiocStyle issue

[Andrzej Oleś]

Dear all,

the compatibility issue with rmarkdown 1.2 have been resolved in
https://github.com/Bioconductor-mirror/BiocStyle/commit/307ad19

Guangchuang, thank you for the heads up on the problem. Even though I was
aware of the incompatibility with rmarkdown release candidate, I couldn't
address it in BiocStyle before rmarkdown 1.2 was released (which happened
only a day ago). Also, please note that the internal changes in rmarkdown
were more complex than only the change of interface to
`rmarkdown:::pandoc_html_highlight_args`, so in order to fix this edits in
multiple places and files were necessary. Regarding the use of `:::`, I'm
currently reviewing the package code in order to avoid it's use if possible.

Best,
Andrzej

On Wed, Nov 23, 2016 at 8:49 AM, Yu, Guangchuang <gcyu at connect.hku.hk>
wrote:

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

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