Thank you for the fixes, I'm having no issues in the release version. However I am still getting a vignette error in tokay2 (from Tuesdays build) which is a bit different from the previous zero-length error:
! Package ifvtex Error: Name clash, \ifvtex is already defined. Thanks, BT On Wed, 2019-12-11 at 00:37 -0500, Simina Boca wrote: > 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 > > > > > > > > > > > > > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
