Maybe others will have better suggestions for how to debug exactly... I am able to reproduce the error and just with a trial and error of deleting and adding chunks of the vignette ... it first seems to appear with the attempt to add the figure
\begin{figure} <<cometwebPlot, echo=FALSE, fig.keep='last',fig.width=7, fig.height=7 >>= extdata <- system.file("extdata", package="coMET",mustWork=TRUE) myinfofile <- file.path(extdata, "cyp1b1_infofile_Grch38.txt") myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region_Grch38.txt") mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt") configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver_Grch38.txt") comet.web(config.file=configfile, mydata.file=myinfofile, cormatrix.file=mycorrelation ,mydata.large.file=myexpressfile, print.image=FALSE,verbose=FALSE) @ %\incfig{fig:cometweb_simple}{\textwidth}{Plot with comet.web function.} \caption{Plot with \Rfunction{comet.web} function.\label{fig:cometweb_simple}} \end{figure} Everything before this seems to R CMD build without this error appearing... Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Martin, Tiphaine <tiphaine.mar...@mssm.edu> Sent: Monday, December 17, 2018 11:31:49 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] failling to build vignette Hi, I need to advise to build my vignette. It seems that my vignette could not build under Bioconductor 3.9. I try to find where it fails, but I don't find the bug. I updated my vignette last February to work with new version of BiocStyle and it did well for Bioconductor 3.8, but it seems that my vignette fails again (http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/) . Could you tell me if there is a major update in BiocStyle or how I can find my bug? Thanks, Tiphaine ----------------------------------------------- Tiphaine Martin, PhD Postdoc Fellow Parsons lab Department of Oncological Sciences The Tisch Cancer Institute at Mount Sinai Icahn School of Medicine at Mount Sinai Hess Center for Science and Medicine 1470 Madison Ave, 6th Floor New York, NY 10029 tel: 1- 212-824-8403 Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel