* using log directory 'd:/Rcompile/CRANpkg/local/3.2/BioGeoBEARS.Rcheck'
* using R version 3.2.5 (2016-04-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'BioGeoBEARS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioGeoBEARS' version '0.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BioGeoBEARS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [11s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs