[Bioc-devel] Error in Vignette of package

Benjamin Jean-Marie Tremblay b2tremb|@y @end|ng |rom uw@ter|oo@c@
Sun Dec 1 16:55:08 CET 2019


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 <iova89 using 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.bioc using gmail.com>
> Sendt: søndag 1. desember 2019 11:51
> Til: Benjamin Jean-Marie Tremblay <b2tremblay using uwaterloo.ca>; Ioannis Vardaxis <iova89 using hotmail.com>
> Kopi: bioc-devel using r-project.org <bioc-devel using 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-bounces using r-project.org on behalf of b2tremblay using 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 <iova89 using 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]]
>     > 
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