[Bioc-devel] failling to build vignette

[Martin, Tiphaine]

Thanks! I am working to fix that!

Tiphaine

----------------------------------------------------------------
Tiphaine Martin
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.martin using mssm.edu

________________________________
From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel using r-project.org
Subject: Re: failling to build vignette


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-bounces using r-project.org> on behalf of Martin, Tiphaine <tiphaine.martin using mssm.edu>
Sent: Monday, December 17, 2018 11:31:49 AM
To: bioc-devel using 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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_coMET_&d=DwMFAg&c=shNJtf5dKgNcPZ6Yh64b-A&r=BH3UNPUNhOc-niJT9d00EAx3ah5AHfQlhQQ_SHtjigA&m=dBNAJlpvc6U1QE6A0BaRRT_a3bMHRDe0DhDvCD_u4TM&s=tN1M5zjUQsGXBvBp3kfL-FiPmfWXaSXZaRIr0mieqy0&e=>) .
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.martin using mssm.edu<mailto:tiphaine.martin using mssm.edu%3E


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