All the "VerbBar" LaTeX errors have cleared up in release and devel. Thanks again Andrzej!
Cheers, H. On 12/6/19 12:17, Hervé Pagès 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