Re: [R] rggobi is crashing R-2.7.0

From: Mark Kimpel <mwkimpel_at_gmail.com>
Date: Wed, 07 May 2008 02:11:26 -0400

Hard as it is for me to imagine, the ggobi windows stay open and functional while R (in emacs) has crashed in the background after throwing the error messages. As a perhaps naive Linux user, I thought that if a parent process crashed any processes it spawned would crash too. I guess not in this case.

Ubuntu currently is distributing graphviz 2.16.1

Thanks,
Mark

On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence <mflawren_at_fhcrc.org> wrote:

>
>
> On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel <mwkimpel@gmail.com> wrote:
>
> > R crashed just after the warnings were issued, but ggobi kept running
> > (if that makes sense).
>
>
> I am not sure if that makes sense; GGobi should exit when the R process
> does.
>
> I have Graphviz and Rgraphiz installed and use Rgraphviz regularly without
> > a problem, so I'm not sure why it didn't load. Mark
> >
>
> Which version of graphviz? I am not sure which version the Ubuntu binary
> expects, but this may be a binary compatibility issue.
>
> That said, I am not sure if the GraphLayout plugin is the reason for R
> crashing...
>
>
> >
> >
> > On Tue, May 6, 2008 at 4:37 PM, Michael Lawrence <mflawren_at_fhcrc.org>
> > wrote:
> >
> > >
> > >
> > > On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel <mwkimpel_at_gmail.com>
> > > wrote:
> > >
> > > > I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the
> > > > interactive
> > > > graph displays but R crashes. See my sessionInfo() and a short
> > > > example
> > > > below. Ggobi and rggobi installed without complaints. Mark
> > > >
> > > > > sessionInfo()
> > > > R version 2.7.0 Patched (2008-05-04 r45620)
> > > > x86_64-unknown-linux-gnu
> > > >
> > > > locale:
> > > >
> > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> > > >
> > > > attached base packages:
> > > > [1] stats graphics grDevices utils datasets methods base
> > > >
> > > > other attached packages:
> > > > [1] rggobi_2.1.9 RGtk2_2.12.5-3 graph_1.18.0
> > > >
> > > > loaded via a namespace (and not attached):
> > > > [1] cluster_1.11.10 tools_2.7.0
> > > >
> > > >
> > > > > a <- matrix(rnorm(1000), nrow = 10)
> > > >
> > > > > g <- ggobi(a)
> > > >
> > > > ** (R:25146): CRITICAL **: Error on loading plugin library
> > > > plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared
> > > > object file:
> > > > No such file or directory
> > > >
> > > > ** (R:25146): CRITICAL **: Error on loading plugin library
> > > > plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared
> > > > object file:
> > > > No such file or directory
> > > >
> > > > ** (R:25146): CRITICAL **: can't locate required plugin routine
> > > > addToToolsMenu in GraphLayout
> > > > >
> > > >
> > >
> > > It's not clear to me - did R crash or did you just receive these
> > > warnings? These warnings are due to a missing graphviz, so the GraphLayout
> > > plugin fails to load.
> > >
> > >
> > > >
> > > > --
> > > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > > > Indiana University School of Medicine
> > > >
> > > > 15032 Hunter Court, Westfield, IN 46074
> > > >
> > > > (317) 490-5129 Work, & Mobile & VoiceMail
> > > > (317) 663-0513 Home (no voice mail please)
> > > >
> > > > ******************************************************************
> > > >
> > > > [[alternative HTML version deleted]]
> > > >
> > > > ______________________________________________
> > > > R-help_at_r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide
> > > > http://www.R-project.org/posting-guide.html
> > > > and provide commented, minimal, self-contained, reproducible code.
> > > >
> > >
> > >
> >
> >
> > --
> > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > Indiana University School of Medicine
> >
> > 15032 Hunter Court, Westfield, IN 46074
> >
> > (317) 490-5129 Work, & Mobile & VoiceMail
> > (317) 663-0513 Home (no voice mail please)
> >
> > ******************************************************************
> >
>
>

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

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Received on Wed 07 May 2008 - 06:15:31 GMT

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