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.mar...@mssm.edu
________________________________
From: Shepherd, Lori <lori.sheph...@roswellpark.org>
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel@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-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/<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.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu%3E
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