[Bioc-devel] Error in Vignette of package

[Simina Boca]

The tokay error is fixed now. Thank you all! Sergio, best wishes for
getting the other error fixed as well!

Cheers,
Simina

On Mon, Dec 9, 2019 at 5:25 PM Sergio Picart Armada <sergi.picart using upc.edu>
wrote:

> Hi all,
>
> I've also followed this thread as the FELLA package has problems with the
> vignette as well.
> I have two issues (link
> <http://bioconductor.org/checkResults/devel/bioc-LATEST/FELLA/tokay2-buildsrc.html>
> )
> First:
>
> Invalid Parameter - /figure-html
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-12-1.png"' execution failed with error code 4
> Invalid Parameter - /figure-html
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "quickstart_files/figure-html/unnamed-chunk-13-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-13-1.png"' execution failed with error code 4
> Invalid Parameter - /figure-html
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "quickstart_files/figure-html/unnamed-chunk-14-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-14-1.png"' execution failed with error code 4
> --- finished re-building 'quickstart.Rmd'
>
> (but I believe this one does not prevent the vignette from building) And the second:
>
> Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
> argument is of length zero
>
> This is the same one reported by Simina, in tokay2 too.
>
> I hope the new adjustement fixes at least the second one.
>
> Thank you Andrzej,
> Sergi
> ​​​​​​
>
> On Monday, December 09, 2019 11:37 CET, Andrzej Oleś <
> andrzej.oles using gmail.com> wrote:
>
>
> Hi Simina,
>
> thank you for reporting the remaining problem on Windows builders. I have
> just made an adjustment to BiocStyle which should resolve the issue.
>
> Cheers,
> Andrzej
>
> On Sun, Dec 8, 2019 at 4:18 PM Simina Boca <smb310 using georgetown.edu> wrote:
>
> > 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]]
> >> >>>>> >
> >> >>>>> > _______________________________________________
> >> >>>>> > Bioc-devel using r-project.org mailing list
> >> >>>>> >
> >>
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> >> >>>>>
> >> >>>>> _______________________________________________
> >> >>>>> Bioc-devel using r-project.org mailing list
> >> >>>>>
> >>
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> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> Bioc-devel using r-project.org mailing list
> >> >>>>
> >>
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> >> >>>>
> >> >>>
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioc-devel using r-project.org mailing list
> >> >
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=
> >> >
> >>
> >> --
> >> Hervé Pagès
> >>
> >> Program in Computational Biology
> >> Division of Public Health Sciences
> >> Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N, M1-B514
> >> P.O. Box 19024
> >> Seattle, WA 98109-1024
> >>
> >> E-mail: hpages using fredhutch.org
> >> Phone: (206) 667-5791
> >> Fax: (206) 667-1319
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> > --
> > 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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>
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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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