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

[Kasper Daniel Hansen]

I got the files, thanks.  I can confirm the crash, but I also get

> tmp = agread("country-graph.dot", layout = FALSE)
> tmp
[1] "A graph with 0 nodes."

(it crashes with layout=TRUE, presumably because it thinks there are
zero nodes).

I also get a crash when I used command-line dot from Graphviz 2.28.0.

I'll look some more, but my guess still stands: it is an invalid dot file.

Kasper

On Tue, Oct 16, 2012 at 12:41 PM, Sam Steingold <sds at gnu.org> wrote:
>> * Kasper Daniel Hansen <xunafra at wufcu.rqh> [2012-10-16 11:23:35 -0400]:
>>
>>> 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.
>
> I attached the file to the message you are replying to, but, apparently,
> bioconductor stripped it.
> Here you go again:
>
>
> PS. I CCed the message to the igraph mailing list to ensure that they
> are in the loop.
>
> --
> Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X 11.0.11103000
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