ggtree

Package: ggtree
Type: Package
Title: a phylogenetic tree viewer for different types of tree
annotations
Version: 1.4.9
Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: ggtree extends the ggplot2 plotting system which implemented the
grammar of graphics. ggtree is designed for visualizing phylogenetic tree
and different types of associated annotation data.
Depends: R (>= 3.2.0), ggplot2 (>= 2.0.0)
Imports: ape, Biostrings, grDevices, grid, jsonlite, magrittr, methods,
stats4, tidyr, utils
Suggests: colorspace, EBImage, knitr, phylobase, phytools, phangorn,
rmarkdown, scales, testthat
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
URL: http://guangchuangyu.github.io/ggtree
BugReports: https://github.com/GuangchuangYu/ggtree/issues
Packaged: 2016-06-26 05:56:04 UTC; biocbuild
biocViews: Alignment, Annotation, Clustering, DataImport,
MultipleSequenceAlignment, ReproducibleResearch, Software,
Visualization
RoxygenNote: 5.0.1
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ggtree' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
Note: wrong number of arguments to '>' 
** help
*** installing help indices
  converting help for package 'ggtree'
    finding HTML links ... done
    Date2decimal                            html  
    MRCA                                    html  
    NJ                                      html  
    add-TREEDATA                            html  
    add_colorbar                            html  
    annotation_image                        html  
    apeBoot                                 html  
    apeBootstrap-class                      html  
    as.binary                               html  
    as.data.frame.phylo                     html  
    beast-class                             html  
    codeml-class                            html  
    codeml_mlc-class                        html  
    collapse                                html  
    decimal2Date                            html  
    dotFun                                  html  
    download.phylopic                       html  
    expand                                  html  
    flip                                    html  
    fortify                                 html  
    geom_aline                              html  
    geom_balance                            html  
    geom_cladelabel                         html  
    geom_hilight                            html  
    geom_label2                             html  
Rd warning: /tmp/Rtmp81smX0/R.INSTALL327237d79a50/ggtree/man/geom_label2.Rd:48: missing file link 'geom_label'
    geom_nodepoint                          html  
    geom_point2                             html  
    geom_range                              html  
    geom_rootpoint                          html  
    geom_segment2                           html  
    geom_strip                              html  
    geom_taxalink                           html  
    geom_text2                              html  
    geom_tiplab                             html  
    geom_tiplab2                            html  
    geom_tippoint                           html  
    geom_tree                               html  
    geom_tree2                              html  
    geom_treescale                          html  
    get.fields-methods                      html  
    get.offspring.tip                       html  
    get.path                                html  
    get.phylopic                            html  
    get.placements-methods                  html  
    get.subs-methods                        html  
    get.tipseq-methods                      html  
    get.tree-methods                        html  
    get.treeinfo-methods                    html  
    get.treetext-methods                    html  
    getNodeNum                              html  
    getRoot                                 html  
    get_balance_position                    html  
    get_clade_position                      html  
    get_heatmap_column_position             html  
    get_taxa_name                           html  
    ggtree-ggproto                          html  
    ggtree                                  html  
    gheatmap                                html  
    groupClade-methods                      html  
    groupOTU-methods                        html  
    groupOTU.phylo                          html  
    gzoom-methods                           html  
    gzoom.phylo                             html  
    hyphy-class                             html  
    inset                                   html  
    jplace-class                            html  
    mask                                    html  
    merge_tree                              html  
    msaplot                                 html  
    multiplot                               html  
    nhx-class                               html  
    nodebar                                 html  
    nodepie                                 html  
    open_tree                               html  
    paml_rst-class                          html  
    phangorn-class                          html  
    phyPML                                  html  
    phylip-class                            html  
    phylopic                                html  
    pipe                                    html  
    plot-methods                            html  
    pmlToSeq                                html  
    print.beastList                         html  
    r8s-class                               html  
    raxml-class                             html  
    raxml2nwk                               html  
    read.baseml                             html  
    read.beast                              html  
    read.codeml                             html  
    read.codeml_mlc                         html  
    read.hyphy                              html  
    read.jplace                             html  
    read.nhx                                html  
    read.paml_rst                           html  
    read.phylip                             html  
    read.r8s                                html  
    read.raxml                              html  
    reexports                               html  
    reroot-methods                          html  
    rescale_tree                            html  
    rm.singleton.newick                     html  
    rotate                                  html  
    rotate_tree                             html  
    rtree                                   html  
    scaleClade                              html  
    scale_color-methods                     html  
    scale_x_ggtree                          html  
    show-methods                            html  
    stat_balance                            html  
    stat_hilight                            html  
    subview                                 html  
    theme_inset                             html  
    theme_transparent                       html  
    theme_tree                              html  
    theme_tree2                             html  
    update-TREE                             html  
    viewClade                               html  
    write.jplace                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggtree)
Making 'packages.html' ... done