Franz, Yes, Mac has changed enough recently that installing the dependencies can be a horrific hassle (specifically: the default use of clang instead of gcc).
A couple of options: 1. Install dependencies with homebrew <http://brew.sh/>. 2. Override the default use of clang, and instead use gcc. 3. If all else fails, and it is not too much trouble, use a virtual box, and install/use treePL in some flavour of linux. This should work flawlessly. HTH. JWB. ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu > On 31 Dec, 2014, at 11:34, Franz Krah <f.k...@mailbox.org> wrote: > > Thanks a lot Brian! > Took me the whole day but finally treePL works fine although there were some > difficulties with Yosemite and the version of c++. > > The "tree <- reorder(tree)" trick didn't do the trick. > > Cheers, > Franz > > > >> Brian O'Meara <omeara.br...@gmail.com> hat am 30. Dezember 2014 um 19:56 >> geschrieben: >> >> >> The programs r8s, pathd8, and treepl can all take a phylogram and return a >> chronogram, but they're not within R (though they could be wrapped). You >> could also infer a chronogram from the start using Beast or MrBayes, though >> the large size of the tree may make it difficult. >> >> One simple thing to try before all this, though, is pass your tree through >> a reorder() function call (using default arguments) before passing it to >> chronos: (i.e., >> >> tree <- read.tree("full_Cipres_Data/RAxML_bestTree.tre") >> >> *tree <- reorder(tree) > tree <- chronos(tree, lambda = 1, model = >> "correlated", quiet = FALSE, >> calibration = makeChronosCalib(tree), >> control = chronos.control()) >> >> Sometimes the imported tree structure, while valid, can be an issue for >> ape and I find doing this reordering can fix weird errors. >> >> Best, >> Brian >> >> _______________________________________ >> Brian O'Meara >> Assistant Professor >> Dept. of Ecology & Evolutionary Biology >> U. of Tennessee, Knoxville >> http://www.brianomeara.info >> >> Postdoc collaborators wanted: http://nimbios.org/postdocs/ >> Calendar: http://www.brianomeara.info/calendars/omeara >> >> On Tue, Dec 30, 2014 at 4:18 AM, Franz Krah <f.k...@mailbox.org> wrote: >> >>> Dear all, >>> >>> I used chronos to make a large phylogeny (~3600 species) ultrametric. >>> The tree is rooted and binary. >>> >>> With the following code I get the error: >>> >>> tree <- read.tree("full_Cipres_Data/RAxML_bestTree.tre") >>> tree <- chronos(tree, lambda = 1, model = "correlated", quiet = FALSE, >>> calibration = makeChronosCalib(tree), >>> control = chronos.control()) >>> >>> >>> Error: >>> >>> In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) : >>> NA/NaN function evaluation >>> >>> This error was posted before some times but I didn't find a satisfying >>> answer. >>> >>> I tried out some things but didn't helped: altering the root in different >>> ways, >>> altering the model, altering lambda. The functions worked fine with smaller >>> phylogenies before! >>> >>> Hope someone found a solution! >>> Are there other ways of making my tree ultrametric? >>> >>> Cheers, Franz >>> >>> _______________________________________________ >>> 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/ [[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/
