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" 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 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
Re: [Bioc-devel] Error in Vignette of package
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 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: ... inline_exec -> hook_eval -> withVisible -> eval -> eval
> Execution halted
>
> Should I wait until BiocStyle is updated?
>
> Best,
> Ioannis
>
> Fra: Martin Morgan
> Sendt: søndag 1. desember 2019 11:51
> Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis
>
> Kopi: 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"
> 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 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
Re: [Bioc-devel] Error in Vignette of package
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: ... inline_exec -> hook_eval -> withVisible -> eval -> eval Execution halted Should I wait until BiocStyle is updated? Best, Ioannis Fra: Martin Morgan Sendt: søndag 1. desember 2019 11:51 Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis Kopi: 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" 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 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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
