[Bioc-devel] Error in Vignette of package

[Pages, Herve]

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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