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