Hi, the error seems to be related to some recent changes in the upstream package rmarkdown v1.18. I will give you an update once I know more details.
Cheers, Andrzej On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay < b2tremb...@uwaterloo.ca> wrote: > Not using BiocStyle::pdf_document means you can’t use the helpers/macros. > Try this in a fresh interactive session: > > library(BiocStyle) > rmarkdown::render("yourvignette.Rmd") > > This should make the helpers/macros available. It won’t fix the issue > for passing R CMD check, but at least it’ll confirm what the issue is and > thus you’ll know to wait for BiocStyle to update. > > BT > > > Le 1 déc. 2019 à 10:47, Ioannis Vardaxis <iov...@hotmail.com> a écrit : > > > > Thanks for the answer. However replacing it resulted in another error > for me: > > > > Quitting from lines 2-41 (MACPET.Rmd) > > Error in doc_date() : could not find function "doc_date" > > Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible -> eval > -> eval > > Execution halted > > > > Should I wait until BiocStyle is updated? > > > > Best, > > Ioannis > > > > Fra: Martin Morgan <mtmorgan.b...@gmail.com> > > Sendt: søndag 1. desember 2019 11:51 > > Til: Benjamin Jean-Marie Tremblay <b2tremb...@uwaterloo.ca>; Ioannis > Vardaxis <iov...@hotmail.com> > > Kopi: bioc-devel@r-project.org <bioc-devel@r-project.org> > > Emne: Re: [Bioc-devel] Error in Vignette of package > > > > Thanks for that insight, we'll try to solve the issue with BiocStyle. > > > > Martin > > > > On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie > Tremblay" <bioc-devel-boun...@r-project.org on behalf of > b2tremb...@uwaterloo.ca> wrote: > > > > I’ve been getting the exact same error for compiling the Rmarkdown > > vignettes in my own package. Some partial testing before the weekend > > revealed that in my case the error could be circumvented simply by > not > > using > > > > output: BiocStyle::pdf_document > > > > but instead > > > > output: pdf_document > > > > in the yaml header. I’m not quite sure why, but when BiocStyle is > used > > some of the latex code for code highlighting is repeated, leading to > the > > 'already defined' error. I’ve not updated my package since before > this > > error started. > > > > BT > > > > > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis <iov...@hotmail.com> a > écrit : > > > > > > Hey, > > > > > > I am trying to build my package Vegnette and I get the following > error: > > > > > > ! LaTeX Error: Command \VerbBar already defined. > > > Or name \end... illegal, see p.192 of the manual. > > > > > > I tried to find what this means with no luck. > > > > > > Best, > > > Ioannis > > > > > > > > > [[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 > > _______________________________________________ > 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