Your Newick string is badly formatted. See: plot(t1)
Error in plot.phylo(t1) : there are single (non-splitting) nodes in your tree; you may need to use collapse.singles() On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Dears, > > I'm using extract.clade from ape package and get some issues. I'm using > phytools package to load tree with single clade like above: > > library(phytools) > > t1 <- read.newick(text='(((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2) > E)D),(F1)F)G)R;') > > t2 <- read.newick(text='((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),( > E1,E2)E)D),(F1)F)R; > > When I extract 'F' clade, for instance: > > c1 <- extract.clade(t1, 'F') > > or > > c2 <- extract.clade(t2, 'F') > > I have this error: > > Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT > > I have one tree with mode than 300 tips. When I try extract any clade, I > have the same error. If I repeat the command I have this one: > > *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory corruption: > 0x000000000a3aaa40 *** > > My configurations was: > > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > language R > version.string R version 3.3.3 (2017-03-06) > > phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10) > > I try update R to 3.4 and recompile all my packages, but I get the same > error. > > My new configurations: > > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > language R > version.string R version 3.4.0 (2017-04-21) > > phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10) > > I don't know why I have this error if I can extract with the same commands > some time ago. > > I have the same error if I run in RStudio or in terminal. When I use > RStudio, it abort after the error. > > I try Google, but I don't found nothing that can help me. > > Thank you and best regards, > > Mario > > > .................................................................... > Mario José Marques-Azevedo > Ph.D. Candidate in Ecology > Department of Plant Biology, Institute of Biology > University of Campinas, Campinas, São Paulo, Brazil > https://github.com/mariojose <http://www.github.com/mariojose> > > [[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/ [[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/
