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.martin at mssm.edu<mailto:tiphaine.martin at mssm.edu>
[Bioc-devel] failling to build vignette
3 messages · Shepherd, Lori, Martin, Tiphaine
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 at r-project.org> on behalf of Martin, Tiphaine <tiphaine.martin at mssm.edu>
Sent: Monday, December 17, 2018 11:31:49 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] failling to build vignette
Sent: Monday, December 17, 2018 11:31:49 AM
To: bioc-devel at 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.martin at mssm.edu<mailto:tiphaine.martin at mssm.edu> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at 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.
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 at mssm.edu
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel at r-project.org
Subject: Re: failling to build vignette
Sent: Monday, December 17, 2018 2:41:59 PM
To: Martin, Tiphaine; bioc-devel at 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 at r-project.org> on behalf of Martin, Tiphaine <tiphaine.martin at mssm.edu>
Sent: Monday, December 17, 2018 11:31:49 AM
To: bioc-devel at 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 at mssm.edu<mailto:tiphaine.martin at mssm.edu%3E
[[alternative HTML version deleted]]
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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.