[BioC] Rgraphviz: how to read a \"dot\" file?

[Kasper Daniel Hansen]

On Tue, Oct 16, 2012 at 12:51 AM, Sam Steingold <sds at gnu.org> wrote:
>> * Vincent Carey <fgiwp at punaavat.uneineq.rqh> [2012-10-15 16:36:04 -0400]:
>>
>> try agread()
>
> Thanks for your kind reply.
> Alas, I have encountered two problems with this function:
>
> 1. unlike all the other R functions, it does not understand "~" in
> filenames:
> Error in agread("~/xgraph/share-click/2012-10-09/country-graph.dot") : Requested file does not exit

This should be easy to fix, thanks.

> 2. when I manually expand the path, it segfaults:
>
>  *** caught segfault ***
> address 0x18, cause 'memory not mapped'
>
> Traceback:
>  1: graphLayout(g)
>  2: agread("/home/sds/xgraph/share-click/2012-10-09/country-graph.dot")

Can you send me the dot file?  The segfault probably comes from
Graphviz, suggesting that igraph has produced an invalid file.  It
would of course be nice for us to catch the exception, but I am not
sure I have resources to fix this.

Kasper


>
> sessionInfo:
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  compiler  methods
> [8] base
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
> The dot file in question was written by igraph:
>
>
>
>
> --
> Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X 11.0.11103000
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>
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