Hi Joseph, i accomplished installing treePL by following the instructions on the treePL page (https://github.com/blackrim/treePL/wiki/Installation) but had to install gcc 4.9 and nlopt manually. gcc 4.7 didn't work. The rest worked fine with homebrew!
Cheers, Franz > "Joseph W. Brown" <josep...@umich.edu> hat am 31. Dezember 2014 um 17:46 > geschrieben: > > > 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/ > _______________________________________________ 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/
