Dears, I removed ape 4.1 and install 4.0 version and the problem with my tree is gone. I can extract clade even my tree having singletons. But the problem still occur in example tree, with new error message. With this tree:

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((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; or (((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R; I have this new error: Error in phy$edge[, 2] : incorrect number of dimensions And with this tree: ((((((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R; rsession running infinitely. I need force stop. Best regards, Mario On 1 June 2017 at 16:13, Mario José Marques-Azevedo <mariojm...@gmail.com> wrote: > Dear Eliot, > > Thank you for your answer! My tree is ok, but to plot is needed to > collapse singles, as you said. > > I use ape/phytools to manipulate my tree for date it after with phylocom. > Then, all node is important, including single one. For this, collapse > singletons do not work for me. For instance. > > This trees: > > ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; > > (((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R; > > 'collapsed' is: > > ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R; > > I lost 'F' node, as I said early. D1 is now in 'right' way. > > This tree: > > ((((((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R; > > 'collapsed' is: > > ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D)DE,F1)G; > > I lost 'F', 'R' and 'ABC' node. > > I have a big tree and some families has polytomies. Then, I extract each > family (remove tips of this node), resolve plytomies, and I bind families > tree again. After that, I date tree with phylocon. Phylocon use ages file > with node age, then each node in my tree is important and collapse > singletons would be a lost of information. > > I created one function to help me with extract node because I have issues > using drop.tips (https://github.com/MarioJose/ > r-functions/blob/master/drop.clade.label/example.md). > > As I said, extract.node was working months ago. I don't know if this error > is some updated that I did. > > Best regards, > > Mario > > > > > On 1 June 2017 at 11:41, Eliot Miller <eliot.is...@gmail.com> wrote: > >> 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/