ape prop.part error malloc(): memory corruption
Dear Klaus, Thank you for your answer and good news that ape/phangorn will load tree with singletons! Can I send the tree to your email? My problem with collapse.singles is, for instance, when I have only one genus/specie. I want the node name with genus and a tip name with species. When I collapse, genus node name is removed. For instance: This tree: ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; when 'collapsed' will be: ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R; ?Note that I lost node name 'F'. I don't know why, but month ago I ran extract.clade of my tree without problem. Maybe some update that I did, but I'm not sure. Thank you again! Best regards, Mario ?.................................................................... Mario Jos? Marques-Azevedo Ph.D. Candidate in Ecology Department of Plant Biology, Institute of Biology University of Campinas, Campinas, S?o Paulo, Brazil https://github.com/mariojose?
On 1 June 2017 at 11:17, Klaus Schliep <klaus.schliep at gmail.com> wrote:
Dear Mario, Emmanuel and I are working to allow singletons in ape / phangorn. In the next version will read the tree in with read.tree(). Can you send me your larger tree for testing purposes, as it is one which would fail at the moment? Regards, Klaus On Thu, Jun 1, 2017 at 8:51 AM, Klaus Schliep <klaus.schliep at gmail.com> wrote:
Hi Mario, the problem with your tree is that it contains singleton (nodes of degree 2). Try collapse.singles() before using extract.clade(). Cheers, Klaus On Thu, Jun 1, 2017 at 1:31 AM, Mario Jos? Marques-Azevedo < mariojmaaz at 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 Jos? Marques-Azevedo Ph.D. Candidate in Ecology Department of Plant Biology, Institute of Biology University of Campinas, Campinas, S?o Paulo, Brazil https://github.com/mariojose <http://www.github.com/mariojose> [[alternative HTML version deleted]]
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-- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/
-- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/