[BioC] Rgraphviz: fail to plot

[Håvard Rue]

I removed my local library, and reinstalled everything. Problem
solved ;-)

thanks.
H

On Thu, 2012-01-26 at 12:23 -0800, Martin Morgan wrote:
> On 01/25/2012 10:30 AM, H??vard Rue [guest] wrote:
> >
> > I upgraded Rgraphviz, and now it fails to plot even the first example,
> >
> >> set.seed(123)
> >> V<- letters[1:10]
> >> M<- 1:4
> >> g1<- randomGraph(V, M, 0.2)
> >> plot(g1)
> > Error in as.double(y) :
> >    cannot coerce type 'S4' to vector of type 'double'
> >
> > seems like no 'plot method' is defined for the graph; but this sounds like something else is going on.
> >
> > Anyone with a similar problem?
> >
> > Best
> > H
> >
> >   -- output of sessionInfo():
> >
> > $ R --vanilla
> >
> > R version 2.14.1 (2011-12-22)
> > Copyright (C) 2011 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> > Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> >    Natural language support but running in an English locale
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> >> library(Rgraphviz)
> > Loading required package: graph
> > Loading required package: grid
> >> set.seed(123)
> >> V<- letters[1:10]
> >> M<- 1:4
> >>
> >>
> >> ###################################################
> >> ### code chunk number 2: createGraph2
> >> ###################################################
> >> g1<- randomGraph(V, M, 0.2)
> >> plot(g1)
> > Error in as.double(y) :
> >    cannot coerce type 'S4' to vector of type 'double'
> >> sessionInfo()
> > R version 2.14.1 (2011-12-22)
> > Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> > locale:
> >   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
> >   [3] LC_TIME=en_DK.utf8        LC_COLLATE=en_GB.utf8
> >   [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
> >   [7] LC_PAPER=C                LC_NAME=C
> >   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] grid      stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] Rgraphviz_1.32.0 graph_1.32.0
> >
> > loaded via a namespace (and not attached):
> > [1] lattice_0.20-0 Matrix_1.0-2   pixmap_0.4-11  sp_0.9-91      tools_2.14.1
> 
> This sessionInfo() isn't consistent with R --vanilla followed by 
> library(Rgraphviz) -- lattice, Matrix, pixmap, sp would not be attached. 
> You're right (in a subsequent message) that the problem looks like 
> method dispatch; Rgraphviz::plot(g1) might get what you want but it 
> would be good to have a complete and consistent script / sessionInfo to 
> understand the problem.
> 
> Martin
> 
> >>
> >
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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> 
> 

b
-- 
Håvard Rue
Department of Mathematical Sciences
Norwegian University of Science and Technology
N-7491 Trondheim, Norway
Voice:  +47-7359-3533    URL  : http://www.math.ntnu.no/~hrue  
Mobile: +47-9260-0021    Email: havard.rue at math.ntnu.no

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