# [Bioc-devel] Error in Vignette of package

Benjamin Jean-Marie Tremblay b2tremb|@y @end|ng |rom uw@ter|oo@c@
Wed Dec 11 21:22:18 CET 2019

Thank you for the fixes, I'm having no issues in the release version. However I
am still getting a vignette error in tokay2 (from Tuesdays build) which is a bit
different from the previous zero-length error:

! Package ifvtex Error: Name clash, \ifvtex is already defined.

Thanks,

BT

On Wed, 2019-12-11 at 00:37 -0500, Simina Boca wrote:
> 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,
> > > >
> > > > > > > > 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
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> >
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> >
> > > >
> > > > --
> > > > 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
> > > > _______________________________________________
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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
> > >
> > >
> > >
> > >
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