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 <hpa...@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.o...@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.o...@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 < > >>> b2tremb...@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 <iov...@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.b...@gmail.com> > >>>>> Sendt: søndag 1. desember 2019 11:51 > >>>>> Til: Benjamin Jean-Marie Tremblay <b2tremb...@uwaterloo.ca>; Ioannis > >>>> Vardaxis <iov...@hotmail.com> > >>>>> Kopi: bioc-devel@r-project.org <bioc-devel@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-boun...@r-project.org on behalf of > >>>> b2tremb...@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 <iov...@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@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= > >>>>> > >>>>> _______________________________________________ > >>>>> Bioc-devel@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= > >>>> > >>>> _______________________________________________ > >>>> Bioc-devel@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= > >>>> > >>> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > _______________________________________________ > Bioc-devel@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/ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel