Hi everyone,
I've followed the conversation about the errors in rebuilding the vignettes.
Thanks a lot for your effort on fixing it.
I get the following error on Windows / tokay2 which has not been fixed yet:
http://bioconductor.org/checkResults/devel/bioc-LATEST/hierinf/tokay2-buildsrc.html
t; > > Not using BiocStyle::pdf_document means you can’t use the
> > > >
> > > > helpers/macros.
> > > > > > > > Try this in a fresh interactive session:
> > > > > > > >
> > > > > > > > library(BiocStyle)
>>>>>
>>>>>> Le 1 déc. 2019 à 10:47, Ioannis Vardaxis a écrit
>>>>> :
>>>>>>
>>>>>> Thanks for the answer. However replacing it resulted in another error
>>>>> for me:
>>>>>>
>
>> >>>>
> >> >>>> library(BiocStyle)
> >> >>>> rmarkdown::render("yourvignette.Rmd")
> >> >>>>
> >> >>>> This should make the helpers/macros available. It won’t fix the
> issue
>
gt;>>> 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
>&
;> 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 10:4
annis Vardaxis a
> écrit
> >>>> :
> >>>>>
> >>>>> Thanks for the answer. However replacing it resulted in another error
> >>>> for me:
> >>>>>
> >>>>> Quitting from lines 2-41 (MACPET.Rmd)
> &
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 -
gt;>> 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
>>> &
ec -> hook_eval -> withVisible -> eval
>> -> eval
>> > Execution halted
>> >
>> > Should I wait until BiocStyle is updated?
>> >
>> > Best,
>> > Ioannis
>> >
>> > Fra: Martin Morgan
>> > Sendt: søndag 1. d
pdated?
> >
> > 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
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
ag 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
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 insig
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
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
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