geiger

Package: geiger
Type: Package
Title: Analysis of Evolutionary Diversification
Version: 2.0.6
Date: 2015-09-07
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: Matt Pennell <mwpennell@gmail.com>
Depends: ape (>= 3.0-6), R (>= 2.15.0)
Imports: MASS, mvtnorm, subplex, deSolve (>= 1.7), digest, Rcpp (>=
0.9.0), coda, ncbit, colorspace, methods
LinkingTo: Rcpp
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
License: GPL (>= 2)
URL: http://www.webpages.uidaho.edu/~lukeh/software.html
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2015-09-07 18:19:34 UTC; mwpennell
Repository: CRAN
Date/Publication: 2015-09-07 21:26:42

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'geiger' ...
** package 'geiger' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c APE_reorder_phylo.c -o APE_reorder_phylo.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"  `/home/ddbj/local/lib64/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic  -g -O2  -c branches.cpp -o branches.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c mkn.c -o mkn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c pic.c -o pic.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c util.c -o util.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"  `/home/ddbj/local/lib64/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic  -g -O2  -c utilities.cpp -o utilities.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o geiger.so APE_reorder_phylo.o branches.o mkn.o pic.o util.o utilities.o -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/geiger/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geiger'
    finding HTML links ... done
    aicm                                    html  
    aicw                                    html  
    aov.phylo                               html  
    bd.ms                                   html  
    calibrate.mecca                         html  
    calibrate.rjmcmc                        html  
    congruify.phylo                         html  
    dcount                                  html  
    drop.extinct                            html  
    dtt                                     html  
    fitContinuous                           html  
    fitContinuousMCMC                       html  
    fitDiscrete                             html  
    gbresolve                               html  
    geiger-data                             html  
    geiger-defunct                          html  
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:46: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:47: missing file link 'disparity'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:49: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:54: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:55: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:56: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:60: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:63: missing file link 'load'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:65: missing file link 'drop.random'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:66: missing file link 'bd.km'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:67: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:70: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:71: missing file link 'disparity'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:73: missing file link 'rescale.phylo'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/geiger-defunct.Rd:74: missing file link 'rescale.phylo'
    geiger-examples                         html  
    geiger-internal                         html  
    geiger-package                          html  
    load.rjmcmc                             html  
    make.gbm                                html  
    mecca                                   html  
    medusa                                  html  
    name.check                              html  
    nh.test                                 html  
    nodelabel.phylo                         html  
    plot.medusa                             html  
    pp.mcmc                                 html  
    ratematrix                              html  
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/ratematrix.Rd:14: missing file link 'rescale.phylo'
    rc                                      html  
    rescale                                 html  
    rjmcmc.bm                               html  
    sim.bd                                  html  
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/sim.bd.Rd:21: missing file link 'bd.km'
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/sim.bd.Rd:31: missing file link 'bd.km'
    sim.bdtree                              html  
Rd warning: /tmp/RtmpMhUEdg/R.INSTALL38187889eb0f/geiger/man/sim.bdtree.Rd:36: missing file link 'rbdtree'
    sim.char                                html  
    startingpt.mecca                        html  
    subset.phylo                            html  
    tips                                    html  
    to.auteur                               html  
    treedata                                html  
** building package indices
** testing if installed package can be loaded
* DONE (geiger)
Making 'packages.html' ... done