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.pic...@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.o...@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 <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 > > > > > -- 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
