Re: [R] rggobi is crashing R-2.7.0

From: Michael Lawrence <mflawren_at_fhcrc.org>
Date: Wed, 07 May 2008 01:14:10 -0700

On Tue, May 6, 2008 at 11:11 PM, Mark Kimpel <mwkimpel_at_gmail.com> wrote:

> 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.
>

Well running it within Emacs may explain it. We actually aren't spawning a new GGobi process - just dynamically linking the GGobi library and starting it that way.

> Ubuntu currently is distributing graphviz 2.16.1
>

Do you have libgvc.so.3 on your system?

Michael

> Thanks,
> Mark
>
>
> On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence <mflawren@fhcrc.org>
> wrote:
>
> >
> >
> > On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel <mwkimpel_at_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)
>
> ******************************************************************
>

        [[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. Received on Wed 07 May 2008 - 08:34:59 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 07 May 2008 - 09:30:35 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive