...it turns out the fatal error was caused by taxon numbering issues - basically, my tree was stored in nexus format and my taxon numbering under "translate" in the trees block were not continuous - I think some were pruned but the numbering still reflected those in the full original tree. I got this resolved using BayesTrees ( http://www.evolution.rdg.ac.uk/BayesTrees.html) and renumbering the taxa. Just out of curiosity, is there a recommended way to deal with this?
thanks, Manabu On 28 October 2016 at 21:00, David Bapst <dwba...@gmail.com> wrote: > Manabu- > > Can you give us a reproducible example? Is it as simple as plotting > any tree does it or is it only particular trees? > > Cheers, > -Dave > > On Fri, Oct 28, 2016 at 7:53 AM, Manabu Sakamoto > <manabu.sakam...@gmail.com> wrote: > > Dear List, > > > > I'm getting fatal errors when plotting phylo objects, which terminates > the > > RStudio session. > > RStudio started showing me warnings from around last week or so, stating > > that something was wrong and that if it wasn't fixed, it will be fatal in > > the next update. I haven't updated R or RStudio but it's turned fatal. > > > > The following error message appears if I use just plain R and not > RStudio: > > > > *** caught segfault *** > > address 0x7fb99a1d8218, cause 'memory not mapped' > > > > Traceback: > > 1: .C(neworder_phylo, as.integer(nb.tip), as.integer(x$edge[, 1]), > > as.integer(x$edge[, 2]), as.integer(nb.edge), integer(nb.edge), io, > > NAOK = TRUE) > > 2: reorder.phylo(x, order = "postorder") > > 3: reorder(x, order = "postorder") > > 4: plot.phylo(tree, show.tip.label = F) > > 5: plot(tree, show.tip.label = F) > > > > Possible actions: > > 1: abort (with core dump, if enabled) > > 2: normal R exit > > 3: exit R without saving workspace > > 4: exit R saving workspace > > > > Has anyone been encountering this issue, or know what the cause is? > > > > thanks, > > Manabu > > -- > > Manabu Sakamoto, PhD > > manabu.sakam...@gmail.com > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > > > -- > David W. Bapst, PhD > Adjunct Asst. Professor, Geology and Geol. Eng. > South Dakota School of Mines and Technology > 501 E. St. Joseph > Rapid City, SD 57701 > > http://webpages.sdsmt.edu/~dbapst/ > http://cran.r-project.org/web/packages/paleotree/index.html > -- Manabu Sakamoto, PhD manabu.sakam...@gmail.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
