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>-- 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]]
On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel <mwkimpel@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@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. >[[alternative HTML version deleted]]
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@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@fhcrc.org> > > wrote: > > > > > > > > > > > On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel <mwkimpel@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@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]]
On Tue, May 6, 2008 at 12:32 PM, 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 >In the R 2.7 release notes, there is a comment about a change in the GUI libraries and it says that one must recompile everything that relies on R. If your R 2.7 was an upgrade, not a fresh install, it could explain why this is happening. If there's some old library or R package sitting around, it could account for this. The part that concerned me about the R release note is that they don't give a very clear guide on how far back in the toolchain we are supposed to go. Certainly, ggobi has to be rebuilt from scratch. But are any of the things on which ggobi depends needing recompliation as well. pj -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas