[Bioc-devel] Error in Vignette of package

[Andrzej Oleś]

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 <
b2tremblay using 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 <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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> >
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