phylobase

Package: phylobase
Type: Package
Title: Base Package for Phylogenetic Structures and Comparative Data
Version: 0.8.2
Imports: ade4, ape (>= 3.0), Rcpp (>= 0.11.0), rncl (>= 0.6.0), grid,
methods, stats, RNeXML
LinkingTo: Rcpp
Suggests: MASS, testthat (>= 0.8.1), knitr
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
License: GPL (>= 2)
URL: https://github.com/fmichonneau/phylobase
BugReports: https://github.com/fmichonneau/phylobase/issues
LazyData: true
Collate: 'oldclasses-class.R' 'internal-constructors.R'
'phylo4-methods.R' 'RcppExports.R' 'checkdata.R'
'phylo4-class.R' 'getNode-methods.R' 'formatData.R'
'phylo4d-class.R' 'phylo4d-methods.R' 'MRCA-methods.R'
'addData-methods.R' 'ancestors.R' 'phylo4-accessors.R'
'root-methods.R' 'nodeId-methods.R' 'edgeLength-methods.R'
'setAs-methods.R' 'extractTree.R' 'labels-methods.R'
'multiphylo4-class.R' 'pdata.R' 'phylo4d-accessors.R'
'phylobase-package.R' 'phylobase.options.R' 'phylomats-class.R'
'print-methods.R' 'readNCL.R' 'reorder-methods.R'
'shortestPath-methods.R' 'subset-methods.R' 'summary-methods.R'
'tbind.R' 'tdata-methods.R' 'treePlot.R' 'treestruc.R' 'zzz.R'
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-01-22 16:13:13 UTC; francois
Repository: CRAN
Date/Publication: 2016-01-23 00:32:41

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'phylobase' ...
** package 'phylobase' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c ancestors.c -o ancestors.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c checkPhylo4.cpp -o checkPhylo4.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c descendants.c -o descendants.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c phyloXX.c -o phyloXX.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c reorderBinary.c -o reorderBinary.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c reorderRobust.c -o reorderRobust.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o phylobase.so RcppExports.o ancestors.o checkPhylo4.o descendants.o phyloXX.o reorderBinary.o reorderRobust.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/phylobase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'edges' in package 'phylobase'
** help
*** installing help indices
  converting help for package 'phylobase'
    finding HTML links ... done
    MRCA                                    html  
    addData-methods                         html  
    ancestors                               html  
    checkPhylo4                             html  
    edgeLength-methods                      html  
    edges-accessors                         html  
    extractTree                             html  
    formatData                              html  
    geospiza                                html  
    getNode-methods                         html  
    labels-methods                          html  
    multiPhylo-class                        html  
    nTips-methods                           html  
    nodeId-methods                          html  
    owls4                                   html  
    pdata-class                             html  
    pdata                                   html  
    phylo4-class                            html  
    phylo4-methods                          html  
    phylo4d-accessors                       html  
    phylo4d-class                           html  
    phylo4d-methods                         html  
    phyloXXYY                               html  
    phylobase-package                       html  
    phylobase.options                       html  
    phylobubbles                            html  
    phylomat-class                          html  
    plotOneTree                             html  
    print-methods                           html  
    readNexus                               html  
    reorder-methods                         html  
    root-methods                            html  
    setAs-methods                           html  
    shortestPath-methods                    html  
    subset-methods                          html  
    summary-methods                         html  
    tdata-methods                           html  
    tip.data.plot                           html  
    treePlot-methods                        html  
    treeStructure-methods                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phylobase)
Making 'packages.html' ... done