[BioC] Rgraphviz: fail to plot

[Dan Tenenbaum]

On Thu, Jan 26, 2012 at 9:53 AM, Håvard Rue <hrue at math.ntnu.no> wrote:
> On Wed, 2012-01-25 at 15:08 -0800, Dan Tenenbaum wrote:
>
>> Are you still having the problem with Rgraphviz?
>> I'm not sure what to tell you. Did you upgrade anything else besides
>> Rgraphviz (such as R itself)? Any difference in how you are running R
>> (for example, are you ssh'd in or are you right at the machine?).
>
>
> this stopped working some months ago, and I have upgraded my system to
> Fedora 16 inbetween.

Did it stop working before or after the OS upgrade?


>
> to me it seems that it does not know that
>
>> class(g1)
> [1] "graphNEL"
> attr(,"package")
> [1] "graph"
>
>
> objects, as a spesific plot-function in Rgraphviz.
>
> I'm not very very into classes/methods, so I might be wrong.
>
> The debug(plot) shows what is going on, I think:
>
>
> $ 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
>> V <- letters[1:10]
>> M <- 1:4
>> g1 <- randomGraph(V, M, 0.2)
>> methods("plot")
>  [1] plot.acf*           plot.data.frame*    plot.decomposed.ts*
>  [4] plot.default        plot.dendrogram*    plot.density
>  [7] plot.ecdf           plot.factor*        plot.formula*
> [10] plot.function       plot.hclust*        plot.histogram*
> [13] plot.HoltWinters*   plot.isoreg*        plot.lm
> [16] plot.medpolish*     plot.mlm            plot.ppr*
> [19] plot.prcomp*        plot.princomp*      plot.profile.nls*
> [22] plot.shingle*       plot.spec           plot.stepfun
> [25] plot.stl*           plot.table*         plot.trellis*
> [28] plot.ts             plot.tskernel*      plot.TukeyHSD
>
>   Non-visible functions are asterisked
>> debug(plot)
>> plot(g1)
> debugging in: plot(g1)
> debug: UseMethod("plot")
> Browse[2]> n
> debugging in: plot.default(g1)
> debug: {
>    localAxis <- function(..., col, bg, pch, cex, lty, lwd) Axis(...)
>    localBox <- function(..., col, bg, pch, cex, lty, lwd) box(...)
>    localWindow <- function(..., col, bg, pch, cex, lty, lwd)
> plot.window(...)
>    localTitle <- function(..., col, bg, pch, cex, lty, lwd) title(...)
>    xlabel <- if (!missing(x))
>        deparse(substitute(x))
>    ylabel <- if (!missing(y))
>        deparse(substitute(y))
>
>

I'm not sure what to make of this.
Perhaps someone else on the list (or the package maintainer, CC'd) can help.

Dan



>
> Best
> H
>
>
>
>
> --
> 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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