[BioC] Rgraphviz: fail to plot

[Martin Morgan]

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

>>
>
>
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