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-phylo@r-project.org/
