Dne St 5. listopadu 2014 13:39:49 jste napsal(a): > Hi I installed and used 1.3 recently (under Ubuntu 14.04). I am no expert > and I can help you further but I wanted to assure you the package is > working fine. I am currently using RStudio and this interface sometimes > makes installing packages easier.
Interesting. Which version was it? I've got more general error, I'd say, it seems like some problem with original archive... > I couldn't compile mp-est which is another option for spp trees. I didn't find package of that name (BioC, CRAN, R-Forge), do You, please, have some reference? > best > > Andrés Thank You, Vojtěch > 2014-11-05 13:03 GMT-02:00 Vojtěch Zeisek <vo...@trapa.cz>: > > Hello, > > I'm looking for approaches how to get a species tree from set of gene > > trees. I > > was looking at Phybase package https://code.google.com/p/phybase/ but it > > seems > > to be abandoned and when I tried to install it, I ended up with error: > > install.packages("~/stazene/phybase_1.3.tar.gz", repos=NULL, > > type="source") > > Installing package into ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.1’ > > (as ‘lib’ is unspecified) > > * installing *source* package ‘phybase’ ... > > ERROR: a 'NAMESPACE' file is required > > * removing ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.1/phybase’ > > Warning in install.packages : > > installation of package ‘/home/vojta/stazene/phybase_1.3.tar.gz’ had > > non- > > zero exit status > > I'm working on Linux. Well, I have gene trees (in multiPhylo object). I > > tried > > superTree, densiTree and speciesTree from phangorn. Those are looking very > > well, but I'd like to try some coalescence based approach. I was looking > > at > > coalSpeciesTree from phangorn, but I don't know how to supply that X > > phyDat > > object - my gene trees have all same tips and species are same in all > > trees. > > How to define it? Or is there any other better approach how to get species > > tree out of gene trees? > > Sincerely, > > Vojtěch -- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
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