[Bioc-devel] Error in Vignette of package

Wed Dec 11 20:17:46 CET 2019

All the "VerbBar" LaTeX errors have cleared up in release and devel. 
Thanks again Andrzej!

Cheers,
H.

On 12/6/19 12:17, Hervé Pagès wrote:
> Great news Andrzej! We'll keep a close eye on the build reports in the 
> next few days. Fingers crossed. Thanks!
> 
> H.
> 
> 
> On 12/6/19 03:46, Andrzej Oleś wrote:
>> 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]]
>>>>>>      >
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> 

-- 
Hervé Pagès

Program in Computational Biology
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