CRAN Package Check Results for Package BioGeoBEARS

Last updated on 2015-07-05 14:46:23.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.1 13.11 87.36 100.47 NOTE
r-devel-linux-x86_64-debian-gcc 0.2.1 13.45 86.85 100.30 NOTE
r-devel-linux-x86_64-fedora-clang 0.2.1 202.02 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2.1 189.15 NOTE
r-devel-osx-x86_64-clang 0.2.1 171.07 NOTE
r-devel-windows-ix86+x86_64 0.2.1 38.00 139.00 177.00 NOTE
r-patched-linux-x86_64 0.2.1 12.78 84.54 97.31 NOTE
r-patched-solaris-sparc 0.2.1 1220.70 NOTE
r-patched-solaris-x86 0.2.1 246.20 NOTE
r-release-linux-x86_64 0.2.1 13.11 85.70 98.82 NOTE
r-release-osx-x86_64-mavericks 0.2.1 NOTE
r-release-windows-ix86+x86_64 0.2.1 43.00 136.00 179.00 NOTE
r-oldrel-windows-ix86+x86_64 0.2.1 63.00 198.00 261.00 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
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