CRAN Package Check Results for Package BioGeoBEARS

Last updated on 2015-08-03 08:48:30.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.1 14.48 98.63 113.11 NOTE
r-devel-linux-x86_64-debian-gcc 0.2.1 14.27 98.72 112.99 NOTE
r-devel-linux-x86_64-fedora-clang 0.2.1 226.02 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2.1 213.94 NOTE
r-devel-osx-x86_64-clang 0.2.1 189.94 NOTE
r-devel-windows-ix86+x86_64 0.2.1 41.00 167.00 208.00 NOTE
r-patched-linux-x86_64 0.2.1 17.25 98.74 115.98 NOTE
r-patched-solaris-sparc 0.2.1 1256.20 NOTE
r-patched-solaris-x86 0.2.1 278.30 NOTE
r-release-linux-x86_64 0.2.1 14.26 97.41 111.66 NOTE
r-release-osx-x86_64-mavericks 0.2.1 NOTE
r-release-windows-ix86+x86_64 0.2.1 54.00 175.00 229.00 NOTE
r-oldrel-windows-ix86+x86_64 0.2.1 61.00 343.00 404.00 NOTE

Check Details

Version: 0.2.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘ape’ ‘cladoRcpp’ ‘phylobase’ ‘rexpokit’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘ape’ ‘cladoRcpp’ ‘methods’ ‘phylobase’ ‘rexpokit’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    ':::' calls which should be '::':
     ‘ape:::floating.pie.asp’ ‘cladoRcpp:::areas_list_to_states_list_old’
     See the note in ?`:::` about the use of this operator.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2.1
Check: R code for possible problems
Result: NOTE
    LGcpp_splits_fn_to_table: no visible global function definition for
     ‘read.table’
    LGcpp_splits_fn_to_table2: no visible global function definition for
     ‘read.table’
    LGcpp_states_fn_to_table: no visible global function definition for
     ‘read.table’
    LGpy_splits_fn_to_table: no visible global function definition for
     ‘read.table’
    areas_list_to_states_list_new: no visible global function definition
     for ‘numstates_from_numareas’
    areas_list_to_states_list_new: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    axisPhylo2: no visible binding for global variable ‘.PlotPhyloEnv’
    axisPhylo2: no visible global function definition for ‘axis’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_DIVA_fast : function_to_optim: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘optim’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘optim’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘optim’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fortest : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘optim’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘optim’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly_simp : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘optim’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_slowQ_slowSP : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘optim’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_3param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘optim’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_3param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘optim’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘read.tree’
    bears_3param_standard_fast_noJ : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘optim’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_4param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_4param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘optim’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘optim’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘read.tree’
    bears_5param_standard_fast_diffstart : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘optim’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘optim’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘read.tree’
    bears_6param_standard_fast_ys_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘optim’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘read.tree’
    bears_9param_standard_fast_ys_v_cb : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘optim’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_optim_run: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_optim_run: no visible global function definition for ‘read.tree’
    bears_optim_run: no visible global function definition for ‘optim’
    bears_optim_run: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_for_optim: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp: no visible global function definition for ‘reorder’
    calc_loglike_sp: no visible global function definition for ‘mat2coo’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘reorder’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘read.tree’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘reorder’
    calc_prob_forward_onebranch_sparse: no visible global function
     definition for ‘expokit_dmexpv_Qmat’
    chainsaw2: no visible global function definition for ‘extract.clade’
    chainsaw2: no visible global function definition for ‘drop.tip’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘is.binary.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘numstates_from_numareas’
    colors_legend: no visible global function definition for ‘plot’
    colors_legend: no visible global function definition for ‘legend’
    cornerlabels: no visible global function definition for ‘par’
    cornerlabels: no visible global function definition for ‘strwidth’
    cornerlabels: no visible global function definition for ‘strheight’
    cornerlabels: no visible global function definition for ‘xinch’
    cornerlabels: no visible global function definition for ‘yinch’
    cornerlabels: no visible global function definition for ‘rect’
    cornerpies: no visible global function definition for ‘par’
    define_BioGeoBEARS_model_object: no visible global function definition
     for ‘new’
    define_tipranges_object: no visible global function definition for
     ‘new’
    get_all_daughter_tips_of_a_node: no visible global function definition
     for ‘extract.clade’
    get_all_node_ages: no visible global function definition for
     ‘dist.nodes’
    get_colors_for_numareas: no visible global function definition for
     ‘rainbow’
    get_colors_for_numareas: no visible global function definition for
     ‘col2rgb’
    get_lagrange_nodenums: no visible global function definition for
     ‘reorder’
    get_node_ages_of_tips: no visible global function definition for
     ‘dist.nodes’
    get_pruningwise_nodenums: no visible global function definition for
     ‘reorder’
    get_statesColors_table: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    given_a_starting_state_simulate_branch_end: no visible global function
     definition for ‘runif’
    given_a_starting_state_simulate_split: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    given_a_starting_state_simulate_split: no visible global function
     definition for ‘runif’
    label_nodes_postorder_phylo3: no visible global function definition for
     ‘as’
    label_nodes_postorder_phylo3: no visible global function definition for
     ‘reorder’
    lrttest: no visible global function definition for ‘pchisq’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘par’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘plot’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘title’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘mtext’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘plot’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘axisPhylo’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘mtext’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘tiplabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘plot’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘mtext’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘par’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘plot’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘title’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘mtext’
    mix_colors_for_states: no visible global function definition for ‘rgb’
    nodenums_bottom_up: no visible global function definition for ‘as’
    nodenums_bottom_up: no visible global function definition for ‘nNodes’
    nodenums_bottom_up: no visible global function definition for ‘nTips’
    nodenums_bottom_up: no visible global function definition for ‘nodeId’
    parse_lagrange_output: no visible global function definition for
     ‘write.table’
    parse_lagrange_output_old: no visible global function definition for
     ‘write.table’
    parse_lagrange_python_output: no visible global function definition for
     ‘write.table’
    parse_lagrange_python_output_old: no visible global function definition
     for ‘write.table’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘layout’
    plot_BioGeoBEARS_model: no visible global function definition for ‘par’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘plot’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘text’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘title’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘barplot’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘axis’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘mtext’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘read.tree’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘reorder’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘numstates_from_numareas’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘plot’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘tiplabels’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘axisPhylo’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘mtext’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘nodelabels’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘title’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘par’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘plot’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘title’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘barplot’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘axis’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘mtext’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘text’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_anclikes_sp_COOweights_faster’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘is’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘as’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘nodeId’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘descendants’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘reorder’
    prune_specimens_to_species: no visible global function definition for
     ‘plot’
    prune_specimens_to_species: no visible global function definition for
     ‘axisPhylo’
    prune_specimens_to_species: no visible global function definition for
     ‘title’
    prune_specimens_to_species: no visible global function definition for
     ‘drop.tip’
    prune_specimens_to_species: no visible global function definition for
     ‘is.ultrametric’
    read_controls: no visible global function definition for ‘read.table’
    read_detections: no visible global function definition for ‘read.table’
    readfiles_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    relative_probabilities_of_subsets: no visible global function
     definition for ‘quantile’
    relative_probabilities_of_vicariants: no visible global function
     definition for ‘median’
    relative_probabilities_of_vicariants: no visible global function
     definition for ‘quantile’
    save_tipranges_to_LagrangePHYLIP: no visible global function definition
     for ‘write.table’
    section_the_tree: no visible global function definition for ‘read.tree’
    section_the_tree: no visible global function definition for ‘plot’
    section_the_tree: no visible global function definition for ‘axisPhylo’
    simulate_biogeog_history: no visible global function definition for
     ‘reorder’
    simulated_indexes_to_tipranges_object: no visible global function
     definition for ‘read.tree’
    simulated_indexes_to_tipranges_object: no visible global function
     definition for ‘reorder’
    traverse_up: no visible global function definition for ‘children’
    Undefined global functions or variables:
     .PlotPhyloEnv as axis axisPhylo barplot children col2rgb descendants
     dist.nodes drop.tip expokit_dgpadm_Qmat expokit_dmexpv_Qmat
     extract.clade is is.binary.tree is.ultrametric layout legend mat2coo
     median mtext nNodes nTips new nodeId nodelabels
     numstates_from_numareas optim par pchisq plot quantile rainbow
     rcpp_areas_list_to_states_list rcpp_calc_anclikes_sp
     rcpp_calc_anclikes_sp_COOprobs
     rcpp_calc_anclikes_sp_COOweights_faster
     rcpp_calc_anclikes_sp_using_COOprobs
     rcpp_calc_rowsums_for_COOweights_columnar
     rcpp_calc_splitlikes_using_COOweights_columnar
     rcpp_states_list_to_DEmat read.table read.tree rect reorder rgb runif
     strheight strwidth text tiplabels title write.table xinch yinch
    Consider adding
     importFrom("grDevices", "col2rgb", "rainbow", "rgb")
     importFrom("graphics", "axis", "barplot", "layout", "legend", "mtext",
     "par", "plot", "rect", "strheight", "strwidth", "text",
     "title", "xinch", "yinch")
     importFrom("methods", "as", "is", "new")
     importFrom("stats", "median", "optim", "pchisq", "quantile", "reorder",
     "runif")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.2.1
Check: R code for possible problems
Result: NOTE
    areas_list_to_states_list_new: no visible global function definition
     for ‘numstates_from_numareas’
    areas_list_to_states_list_new: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    axisPhylo2: no visible binding for global variable ‘.PlotPhyloEnv’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_DIVA_fast : function_to_optim: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fortest : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly_simp : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_slowQ_slowSP : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_3param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_3param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘read.tree’
    bears_3param_standard_fast_noJ : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_4param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_4param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘read.tree’
    bears_5param_standard_fast_diffstart : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘read.tree’
    bears_6param_standard_fast_ys_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘read.tree’
    bears_9param_standard_fast_ys_v_cb : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_optim_run: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_optim_run: no visible global function definition for ‘read.tree’
    bears_optim_run: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_for_optim: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp: no visible global function definition for ‘mat2coo’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘read.tree’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_prob_forward_onebranch_sparse: no visible global function
     definition for ‘expokit_dmexpv_Qmat’
    chainsaw2: no visible global function definition for ‘extract.clade’
    chainsaw2: no visible global function definition for ‘drop.tip’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘is.binary.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘numstates_from_numareas’
    get_all_daughter_tips_of_a_node: no visible global function definition
     for ‘extract.clade’
    get_all_node_ages: no visible global function definition for
     ‘dist.nodes’
    get_node_ages_of_tips: no visible global function definition for
     ‘dist.nodes’
    get_statesColors_table: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    given_a_starting_state_simulate_split: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘axisPhylo’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘tiplabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    nodenums_bottom_up: no visible global function definition for ‘nNodes’
    nodenums_bottom_up: no visible global function definition for ‘nTips’
    nodenums_bottom_up: no visible global function definition for ‘nodeId’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘read.tree’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘numstates_from_numareas’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘tiplabels’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘axisPhylo’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘nodelabels’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_anclikes_sp_COOweights_faster’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘nodeId’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘descendants’
    prune_specimens_to_species: no visible global function definition for
     ‘axisPhylo’
    prune_specimens_to_species: no visible global function definition for
     ‘drop.tip’
    prune_specimens_to_species: no visible global function definition for
     ‘is.ultrametric’
    readfiles_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    section_the_tree: no visible global function definition for ‘read.tree’
    section_the_tree: no visible global function definition for ‘axisPhylo’
    simulated_indexes_to_tipranges_object: no visible global function
     definition for ‘read.tree’
    traverse_up: no visible global function definition for ‘children’
    Undefined global functions or variables:
     .PlotPhyloEnv axisPhylo children descendants dist.nodes drop.tip
     expokit_dgpadm_Qmat expokit_dmexpv_Qmat extract.clade is.binary.tree
     is.ultrametric mat2coo nNodes nTips nodeId nodelabels
     numstates_from_numareas rcpp_areas_list_to_states_list
     rcpp_calc_anclikes_sp rcpp_calc_anclikes_sp_COOprobs
     rcpp_calc_anclikes_sp_COOweights_faster
     rcpp_calc_anclikes_sp_using_COOprobs
     rcpp_calc_rowsums_for_COOweights_columnar
     rcpp_calc_splitlikes_using_COOweights_columnar
     rcpp_states_list_to_DEmat read.tree tiplabels
Flavor: r-devel-osx-x86_64-clang

Version: 0.2.1
Check: R code for possible problems
Result: NOTE
    areas_list_to_states_list_new: no visible global function definition
     for ‘numstates_from_numareas’
    areas_list_to_states_list_new: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    axisPhylo2: no visible binding for global variable ‘.PlotPhyloEnv’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_DIVA_fast : function_to_optim: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_DIVA_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_2param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_fortest : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_fortest: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_fast_symOnly_simp : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_fast_symOnly_simp: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘read.tree’
    bears_2param_standard_slowQ_slowSP : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_2param_standard_slowQ_slowSP: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_3param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_fixnode: no visible global function
     definition for ‘read.tree’
    bears_3param_standard_fast_fixnode : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘read.tree’
    bears_3param_standard_fast_noJ : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_3param_standard_fast_noJ: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_4param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_4param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_4param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘read.tree’
    bears_5param_standard_fast_diffstart : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_diffstart: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘read.tree’
    bears_5param_standard_fast_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_5param_standard_fast_v: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_areas_list_to_states_list’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘read.tree’
    bears_6param_standard_fast_ys_v : function_to_optim: no visible global
     function definition for ‘rcpp_states_list_to_DEmat’
    bears_6param_standard_fast_ys_v: no visible global function definition
     for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘read.tree’
    bears_9param_standard_fast_ys_v_cb : function_to_optim: no visible
     global function definition for ‘rcpp_states_list_to_DEmat’
    bears_9param_standard_fast_ys_v_cb: no visible global function
     definition for ‘rcpp_states_list_to_DEmat’
    bears_optim_run: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    bears_optim_run: no visible global function definition for ‘read.tree’
    bears_optim_run: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_for_optim: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp: no visible global function definition for ‘mat2coo’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dmexpv_Qmat’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_using_COOprobs’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘rcpp_calc_splitlikes_using_COOweights_columnar’
    calc_loglike_sp_prebyte: no visible global function definition for
     ‘expokit_dgpadm_Qmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_states_list_to_DEmat’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘read.tree’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘mat2coo’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_anclikes_sp_COOweights_faster’
    calc_loglike_sp_stratified: no visible global function definition for
     ‘rcpp_calc_rowsums_for_COOweights_columnar’
    calc_prob_forward_onebranch_sparse: no visible global function
     definition for ‘expokit_dmexpv_Qmat’
    chainsaw2: no visible global function definition for ‘extract.clade’
    chainsaw2: no visible global function definition for ‘drop.tip’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘is.binary.tree’
    check_BioGeoBEARS_run: no visible global function definition for
     ‘numstates_from_numareas’
    get_all_daughter_tips_of_a_node: no visible global function definition
     for ‘extract.clade’
    get_all_node_ages: no visible global function definition for
     ‘dist.nodes’
    get_node_ages_of_tips: no visible global function definition for
     ‘dist.nodes’
    get_statesColors_table: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    given_a_starting_state_simulate_split: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LG_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘axisPhylo’
    map_LG_MLsplits_to_tree_corners: no visible global function definition
     for ‘tiplabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘axisPhylo’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LG_MLstates_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘nodelabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘tiplabels’
    map_LGpy_MLsplits_to_tree: no visible global function definition for
     ‘axisPhylo’
    nodenums_bottom_up: no visible global function definition for ‘nNodes’
    nodenums_bottom_up: no visible global function definition for ‘nTips’
    nodenums_bottom_up: no visible global function definition for ‘nodeId’
    plot_BioGeoBEARS_model: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘read.tree’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘numstates_from_numareas’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘rcpp_areas_list_to_states_list’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘tiplabels’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘axisPhylo’
    plot_BioGeoBEARS_results: no visible global function definition for
     ‘nodelabels’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_areas_list_to_states_list’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_anclikes_sp_COOweights_faster’
    plot_cladogenesis_size_probabilities: no visible global function
     definition for ‘rcpp_calc_rowsums_for_COOweights_columnar’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘nodeId’
    postorder_nodes_phylo4_return_table: no visible global function
     definition for ‘descendants’
    prune_specimens_to_species: no visible global function definition for
     ‘axisPhylo’
    prune_specimens_to_species: no visible global function definition for
     ‘drop.tip’
    prune_specimens_to_species: no visible global function definition for
     ‘is.ultrametric’
    readfiles_BioGeoBEARS_run: no visible global function definition for
     ‘read.tree’
    section_the_tree: no visible global function definition for ‘read.tree’
    section_the_tree: no visible global function definition for ‘axisPhylo’
    simulated_indexes_to_tipranges_object: no visible global function
     definition for ‘read.tree’
    traverse_up: no visible global function definition for ‘children’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64