[Bioc-devel] BiocStyle issue

[Andrzej Oleś]

In case someone is wondering: The patch has also been applied in release.
Any packages currently failing with the error

Error: processing vignette 'xxxxxxxxx.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted

should recover with BiocStyle v.2.2.1

Cheers,
Andrzej

On Wed, Nov 23, 2016 at 2:27 PM, Andrzej Oleś <andrzej.oles at gmail.com>
wrote:

> 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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