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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
