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.o...@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 <g...@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 < >> lcoll...@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 <g...@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@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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
