[Bioc-devel] Error in Vignette of package

Simina Boca @mb310 @end|ng |rom georgetown@edu
Sun Dec 8 16:18:07 CET 2019


Hi all,
I've been following this conversation as I was having the same issue for
the swfdr package. Happy to see that it's now fixed on malbec and merida,
though I now see a different error on tokay, also referring to the
vignettes. I looked around a bit, and a bunch of other packages now have
the tokay error, which is:

* creating vignettes ... ERROR
--- re-building 'swfdrQ.Rmd' using rmarkdown
Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'swfdrQ.Rmd'

https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html


Thanks!
Cheers,
Simina



On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages using fredhutch.org> 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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> >>>>>      >
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> >       [[alternative HTML version deleted]]
> >
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> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>
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-- 
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

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