Hi Ben.
Your Newick string has some issues & is possibly invalid. I believe
there are commas missing after "0.0242997" and after "0.475571". If the
line-breaks are eliminated, phytools read.newick will read the string -
but the result is a very peculiar tree. Whereas if I put commas in those
two spots, I obtain an ultrametric tree from read.tree or read.newick.
This may be beside the point if the issue is that this text string when
read using read.tree crashes R rather than producing a more sensible
error. This I too experienced.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/9/2015 9:02 PM, Ben Bolker wrote:
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I came across this in one of my example files. Just thought I'd
report it:
library("ape")
sessionInfo()
## R Under development (unstable) (2015-02-11 r67792)
## Platform: i686-pc-linux-gnu (32-bit)
## Running under: Ubuntu precise (12.04.5 LTS)
## ...
## other attached packages:
## [1] ape_3.2
treeText <- "(((8:0.102773,3:0.102773):0.0537417,((0:0.0242997
(7:0.0205236,2:0.0205236):0.00377606):0.0523697,4:0.0766694):0.0798455):0.475571
((9:0.0099204,5:0.0099204):0.202541,(1:0.00367543,6:0.00367543):0.208786):0.419624);"
tree <- collapse.singles(read.tree(file=textConnection(treeText)))
plot(tree)
*** caught segfault ***
address 0x4d79c0e0, cause 'memory not mapped'
Traceback:
1: .C(node_height, as.integer(Ntip), as.integer(Nnode),
as.integer(edge[, 1]), as.integer(edge[, 2]), as.integer(Nedge),
as.double(yy))
2: .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
3: plot.phylo(tree)
4: plot(tree)
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