[Bioc-devel] Error in Vignette of package

Andrzej Oleś @ndrzej@o|e@ @end|ng |rom gm@||@com
Fri Dec 6 12:46:37 CET 2019


Dear Package Developers,

An updated version of BiocStyle has been deployed to both the development
and the release branch. The fix addresses vignette build errors occurring
with rmarkdown v1.18, these should clear up within the next build cycle.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 2:31 PM Andrzej Oleś <andrzej.oles using gmail.com> wrote:

> Dear Package Developers,
>
> BiocStyle will be patched within the next couple of days to address the
> observed errors. Until then please refrain from making any changes to your
> package, the issue should resolve itself once BiocStyle is updated.
>
> Cheers,
> Andrzej
>
> On Mon, Dec 2, 2019 at 11:20 AM Andrzej Oleś <andrzej.oles using gmail.com>
> wrote:
>
>> 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]]
>>> >     >
>>> >     > _______________________________________________
>>> >     > Bioc-devel using r-project.org mailing list
>>> >     > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>> >     _______________________________________________
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>>>
>>> _______________________________________________
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>>>
>>

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