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
