Gossaye Hailu
2021-May-28 18:55 UTC
[R] Error: C stack usage 15924320 is too close to the limit
I am doing phylogenetic analysis of ecological community data set using Picante package to find out PD, MPD, MNTD I have run the following arguments library(picante)>tree4.phylotree<-read.tree("phylojune2016.edit.phy") >tree4.phy<-read.csv("june2016.matrix.csv",sep=",",header = TRUE,row.names= 1)>tree4.out<-pd(tree4.phy,tree4.phylotree,include.root = FALSE) >tree4.out[,3]<-mpd(tree4.phy,cophenetic(tree4.phylotree)) >tree4.out[,4]<-mntd(tree4.phy,cophenetic(tree4.phylotree)) >names(tree4.out)[3:4]<-c("MPD","MNTD")When I randomize the matrix 999 times the following Error term appears>tree4.mpd<-ses.mpd(tree4.phy,cophenetic(tree4.phylotree),runs = 999)Error: C stack usage 15923904 is too close to the limit How can I solve this error please? I will highly appreciate your help! [[alternative HTML version deleted]]
Bert Gunter
2021-May-29 19:55 UTC
[R] Error: C stack usage 15924320 is too close to the limit
Please see the posting guide linked below. Questions about nonstandard packages are generally off topic here. You should probably do as the pg recommends and contact the maintainer, who you can find by the maintainer() function. Bert On Sat, May 29, 2021, 10:16 AM Gossaye Hailu <gossaye15 at gmail.com> wrote:> I am doing phylogenetic analysis of ecological community data set using > Picante package to find out PD, MPD, MNTD > I have run the following arguments > library(picante) > >tree4.phylotree<-read.tree("phylojune2016.edit.phy") > >tree4.phy<-read.csv("june2016.matrix.csv",sep=",",header = TRUE,row.names > = 1) > >tree4.out<-pd(tree4.phy,tree4.phylotree,include.root = FALSE) > >tree4.out[,3]<-mpd(tree4.phy,cophenetic(tree4.phylotree)) > >tree4.out[,4]<-mntd(tree4.phy,cophenetic(tree4.phylotree)) > >names(tree4.out)[3:4]<-c("MPD","MNTD") > > When I randomize the matrix 999 times the following Error term appears > >tree4.mpd<-ses.mpd(tree4.phy,cophenetic(tree4.phylotree),runs = 999) > > Error: C stack usage 15923904 is too close to the limit > > How can I solve this error please? I will highly appreciate your help! > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Jeff Newmiller
2021-May-29 20:07 UTC
[R] Error: C stack usage 15924320 is too close to the limit
You may need to use smaller data. Anyway, read the Posting Guide, which says for contributed packages to contact the package maintainer ?maintainer On May 28, 2021 11:55:04 AM PDT, Gossaye Hailu <gossaye15 at gmail.com> wrote:>I am doing phylogenetic analysis of ecological community data set using >Picante package to find out PD, MPD, MNTD >I have run the following arguments >library(picante) >>tree4.phylotree<-read.tree("phylojune2016.edit.phy") >>tree4.phy<-read.csv("june2016.matrix.csv",sep=",",header >TRUE,row.names >= 1) >>tree4.out<-pd(tree4.phy,tree4.phylotree,include.root = FALSE) >>tree4.out[,3]<-mpd(tree4.phy,cophenetic(tree4.phylotree)) >>tree4.out[,4]<-mntd(tree4.phy,cophenetic(tree4.phylotree)) >>names(tree4.out)[3:4]<-c("MPD","MNTD") > >When I randomize the matrix 999 times the following Error term appears >>tree4.mpd<-ses.mpd(tree4.phy,cophenetic(tree4.phylotree),runs = 999) > >Error: C stack usage 15923904 is too close to the limit > >How can I solve this error please? I will highly appreciate your help! > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- Sent from my phone. Please excuse my brevity.