-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 (I tried to respond yesterday but Google thought I was sending spam for some reason.)
I totally agree that this is *not* high priority -- I just found it while browsing through some other stuff and thought it should be noted, since crashes are bugs by definition ... thanks Ben On 15-03-10 11:13 AM, Emmanuel Paradis wrote: > Hi, > > Liam is right. > > Some months ago, I wrote a function to help diagnose this kind of > problem. I've put it on GitHub: > > https://github.com/emmanuelparadis/checkValidPhylo > > However, in the present case, it won't tell you where is the > problem in your Newick string. > > Best, > > Emmanuel > > Le 10/03/2015 02:45, Liam J. Revell a écrit : >> 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: > 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) > >>> >>> _______________________________________________ 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/ >>> >> >> _______________________________________________ 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/ >> >> >> >> >> > > _______________________________________________ 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/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJU/xjMAAoJEOCV5YRblxUH17kIAMRiAxIcMELv5C+xC2SyScfJ OstMWkw5Z7jn1EdhhYP2dgFHxyO6HL3nL4OZlSGw2MYTW3dfC2UH2K1RCdGLkJVS 0pOm2LsnzLi+t5XwSkJ9vwotvVF7qSlKabFEhB1/8d0iwB9ff2+HurjOOccDkqh6 FQ6OGKrxdsrvYX9aT2dNwYAijUjKMJ1j0oHZhW3zchJah1L+JSbaK/vxw5X/Qc12 vZSLQr+q0GHMHVklZgO7Lvs9irz/mfoBFxwYRE4Lz2NEfyOOBat40GiBY5AjKj0j vwapu4Q2kYvviQgpLgz80Susf42bBcGesApXXaofHFle/ZlSIcx57VXECDc8FlQ= =THO4 -----END PGP SIGNATURE----- _______________________________________________ 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/
