[BioC] Rgraphviz: fail to plot

[Dan Tenenbaum]

Hi Hávard,

2012/1/25 Håvard Rue [guest] <guest at bioconductor.org>:
>
> 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
>>
>

Not sure what is going on here.
What does
capabilities()
report?

It's always a good idea to make sure all your packages are up to date
as follows:
source("http://bioconductor.org/biocLite.R")
biocLite(character(), ask=FALSE)

Try that and let us know if your results change.
Dan


>
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