taxize

Package: taxize
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as verifying species names, and getting taxonomic 'hierarchies'.
Version: 0.7.8
License: MIT + file LICENSE
URL: https://github.com/ropensci/taxize
BugReports: https://github.com/ropensci/taxize/issues
Authors@R: c(
person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"),
person("Eduard", "Szoecs", role = "aut", email = "eduardszoecs@gmail.com"),
person("Zachary", "Foster", role = "aut", email = "zacharyfoster1989@gmail.com"),
person("Carl", "Boettiger", role = "aut", email = "cboettig@gmail.com"),
person("Karthik", "Ram", role = "aut", email = "karthik@ropensci.org"),
person("Ignasi", "Bartomeus", role = "aut", email = "nacho.bartomeus@gmail.com"),
person("John", "Baumgartner", role = "aut", email = "johnbb@student.unimelb.edu.au"),
person("James", "O'Donnell", role = "aut", email = "jodonnellbio@gmail.com")
)
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
Depends: R (>= 3.2.1)
Imports: graphics, methods, stats, utils, httr (>= 1.1.0), xml2 (>=
0.1.2), jsonlite, reshape2, stringr, plyr, foreach, ape, bold
(>= 0.3.5), data.table, rredlist (>= 0.1.0), rotl (>= 0.5.0)
Suggests: testthat, knitr, vegan, covr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-16 21:14:33 UTC; sacmac
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut],
James O'Donnell [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2016-06-17 08:57:14

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'taxize' ...
** package 'taxize' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'taxize'
    finding HTML links ... done
    apg                                     html  
    apg_families                            html  
    apg_lookup                              html  
    apg_orders                              html  
    bold_search                             html  
    children                                html  
    class2tree                              html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/class2tree.Rd:52: missing file link 'taxa2dist'
    classification                          html  
    col_children                            html  
    col_classification-defunct              html  
    col_downstream                          html  
    col_search                              html  
    comm2sci                                html  
    downstream                              html  
    eol_dataobjects                         html  
    eol_hierarchy-defunct                   html  
    eol_invasive-defunct                    html  
    eol_pages                               html  
    eol_search                              html  
    eubon                                   html  
    fungorum                                html  
    gbif_downstream                         html  
    gbif_name_usage                         html  
    gbif_parse                              html  
    genbank2uid                             html  
    get_boldid                              html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_boldid.Rd:55: missing file link 'get_boldid_'
    get_colid                               html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_colid.Rd:44: missing file link 'get_colid_'
    get_eolid                               html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_eolid.Rd:47: missing file link 'get_eolid_'
    get_gbifid                              html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_gbifid.Rd:46: missing file link 'get_gbifid_'
    get_genes-defunct                       html  
    get_genes_avail-defunct                 html  
    get_ids                                 html  
    get_nbnid                               html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_nbnid.Rd:51: missing file link 'get_nbnid_'
    get_seqs-defunct                        html  
    get_tpsid                               html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_tpsid.Rd:47: missing file link 'get_tpsid_'
    get_tsn                                 html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_tsn.Rd:51: missing file link 'get_tsn_'
    get_ubioid-defunct                      html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_ubioid-defunct.Rd:48: missing file link 'get_ubioid_'
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_ubioid-defunct.Rd:82: missing file link 'ubio_search'
    get_uid                                 html  
Rd warning: /tmp/RtmpngaJgL/R.INSTALL3a41eb1f37a/taxize/man/get_uid.Rd:45: missing file link 'get_uid_'
    getacceptednamesfromtsn                 html  
    getanymatchcount                        html  
    getcommentdetailfromtsn                 html  
    getcommonnamesfromtsn                   html  
    getcoremetadatafromtsn                  html  
    getcoveragefromtsn                      html  
    getcredibilityratingfromtsn             html  
    getcredibilityratings                   html  
    getcurrencyfromtsn                      html  
    getdatedatafromtsn                      html  
    getdescription                          html  
    getexpertsfromtsn                       html  
    getfullhierarchyfromtsn                 html  
    getfullrecordfromlsid                   html  
    getfullrecordfromtsn                    html  
    getgeographicdivisionsfromtsn           html  
    getgeographicvalues                     html  
    getglobalspeciescompletenessfromtsn     html  
    gethierarchydownfromtsn                 html  
    gethierarchyupfromtsn                   html  
    getitisterms                            html  
    getitistermsfromcommonname              html  
    getitistermsfromscientificname          html  
    getjurisdictionaloriginfromtsn          html  
    getjurisdictionoriginvalues             html  
    getjurisdictionvalues                   html  
    getkey                                  html  
    getkingdomnamefromtsn                   html  
    getkingdomnames                         html  
    getlastchangedate                       html  
    getlsidfromtsn                          html  
    getothersourcesfromtsn                  html  
    getparenttsnfromtsn                     html  
    getpublicationsfromtsn                  html  
    getranknames                            html  
    getrecordfromlsid                       html  
    getreviewyearfromtsn                    html  
    getscientificnamefromtsn                html  
    getsynonymnamesfromtsn                  html  
    gettaxonauthorshipfromtsn               html  
    gettaxonomicranknamefromtsn             html  
    gettaxonomicusagefromtsn                html  
    gettsnbyvernacularlanguage              html  
    gettsnfromlsid                          html  
    getunacceptabilityreasonfromtsn         html  
    getvernacularlanguages                  html  
    gisd_invasive-defunct                   html  
    gni_details                             html  
    gni_parse                               html  
    gni_search                              html  
    gnr_datasources                         html  
    gnr_resolve                             html  
    ion                                     html  
    iplant_resolve                          html  
    ipni_search                             html  
    itis-api                                html  
    itis_acceptname                         html  
    itis_downstream                         html  
    itis_getrecord                          html  
    itis_hierarchy                          html  
    itis_kingdomnames                       html  
    itis_lsid                               html  
    itis_name-deprecated                    html  
    itis_native                             html  
    itis_refs                               html  
    itis_searchcommon                       html  
    itis_taxrank                            html  
    itis_terms                              html  
    iucn_getname                            html  
    iucn_id                                 html  
    iucn_status                             html  
    iucn_summary                            html  
    lowest_common                           html  
    names_list                              html  
    nbn_classification                      html  
    nbn_search                              html  
    nbn_synonyms                            html  
    ncbi_children                           html  
    ncbi_get_taxon_summary                  html  
    ncbi_getbyid-defunct                    html  
    ncbi_getbyname-defunct                  html  
    ncbi_search-defunct                     html  
    phylomatic_format-defunct               html  
    phylomatic_tree-defunct                 html  
    ping                                    html  
    plantGenusNames                         html  
    plantNames                              html  
    plantminer                              html  
    rank_ref                                html  
    rankagg                                 html  
    resolve                                 html  
    sci2comm                                html  
    scrapenames                             html  
    searchbycommonname                      html  
    searchbycommonnamebeginswith            html  
    searchbycommonnameendswith              html  
    searchbyscientificname                  html  
    searchforanymatch                       html  
    searchforanymatchpaged                  html  
    status_codes                            html  
    synonyms                                html  
    tax_agg                                 html  
    tax_name                                html  
    tax_rank                                html  
    taxize-defunct                          html  
    taxize-package                          html  
    taxize_capwords                         html  
    taxize_cite                             html  
    taxize_ldfast                           html  
    theplantlist                            html  
    tnrs                                    html  
    tnrs_sources                            html  
    tol_resolve                             html  
    tp_acceptednames-deprecated             html  
    tp_accnames                             html  
    tp_classification-defunct               html  
    tp_dist                                 html  
    tp_namedistributions-deprecated         html  
    tp_namereferences-deprecated            html  
    tp_refs                                 html  
    tp_search                               html  
    tp_summary                              html  
    tp_synonyms                             html  
    tpl_families                            html  
    tpl_get                                 html  
    tpl_search-defunct                      html  
    ubio_classification-defunct             html  
    ubio_classification_search-defunct      html  
    ubio_id-defunct                         html  
    ubio_ping-defunct                       html  
    ubio_search-defunct                     html  
    ubio_synonyms-defunct                   html  
    upstream                                html  
    vascan_search                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (taxize)
Making 'packages.html' ... done