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 <smb...@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 <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
