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
