CRAN Package Check Results for Package BioGeoBEARS

Last updated on 2014-11-22 20:46:49.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.1 17.43 117.82 135.24 NOTE
r-devel-linux-x86_64-debian-gcc 0.2.1 17.02 115.74 132.76 NOTE
r-devel-linux-x86_64-fedora-clang 0.2.1 208.48 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2.1 265.04 NOTE
r-devel-osx-x86_64-clang 0.2.1 173.86 NOTE
r-devel-windows-ix86+x86_64 0.2.1 39.00 228.00 267.00 NOTE
r-patched-linux-x86_64 0.2.1 18.88 120.37 139.25 NOTE
r-patched-solaris-sparc 0.2.1 1100.70 NOTE
r-patched-solaris-x86 0.2.1 357.10 NOTE
r-release-linux-ix86 0.2.1 21.66 145.44 167.10 NOTE
r-release-linux-x86_64 0.2.1 18.58 125.72 144.31 NOTE
r-release-osx-x86_64-mavericks 0.2.1 NOTE
r-release-osx-x86_64-snowleopard 0.2.1 ERROR
r-release-windows-ix86+x86_64 0.2.1 51.00 171.00 222.00 NOTE
r-oldrel-windows-ix86+x86_64 0.2.1 36.00 175.00 211.00 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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
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-ix86, 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
    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-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-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.2.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘phylobase’
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-release-osx-x86_64-snowleopard