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 file (and ensure that your DESCRIPTION Imports field
contains 'methods').