Running ‘testthat.R’ [15s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(occCite)
  > 
  > test_check("occCite")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● GBIF Login information not available (1)
  ● On CRAN (14)
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:18:3): studyTaxonList works with a phylogeny ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = phylogeny, datasources = c("NCBI")) test-studyTaxonList.R:18:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-studyTaxonList.R:45:3): studyTaxonList works with a vector of species ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::studyTaxonList(x = taxVector, datasources = c("NCBI")) test-studyTaxonList.R:45:2
   4. occCite::taxonRectification(taxName = targets[[count]], datasources = datasources)
  ── Warning (test-taxonRectification.R:27:3): taxonRectification performs as expected ──
  The following sources were not found in Global Names Index source list: NCBI
  Backtrace:
   1. occCite::taxonRectification(...) test-taxonRectification.R:27:2
  ── Warning (test-taxonRectification.R:27:3): taxonRectification performs as expected ──
  No valid taxonomic data sources supplied. Populating default list from all available sources.
  Backtrace:
   1. occCite::taxonRectification(...) test-taxonRectification.R:27:2
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-taxonRectification.R:11:3): functions on which it depends function as necessary ──
  "NCBI" %in% sources$title is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-taxonRectification.R:21:3): functions on which it depends function as necessary ──
  nrow(temp) == 1 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-taxonRectification.R:22:3): functions on which it depends function as necessary ──
  temp$user_supplied_name == temp$matched_name is not TRUE
  
  `actual`:   TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE and 31 more...
  `expected`: TRUE                                              ...           
  ── Failure (test-taxonRectification.R:23:3): functions on which it depends function as necessary ──
  temp$data_source_title == datasources is not TRUE
  
       actual | expected                
   [1] FALSE  - TRUE     [1]            
   [2] FALSE  -                         
   [3] FALSE  -                         
   [4] FALSE  -                         
   [5] FALSE  -                         
   [6] FALSE  -                         
   [7] FALSE  -                         
   [8] FALSE  -                         
   [9] FALSE  -                         
  [10] FALSE  -                         
   ... ...      ...      and 31 more ...
  ── Failure (test-taxonRectification.R:36:3): taxonRectification performs as expected ──
  testResult$`Best Match`[1] == "Buteo buteo harterti" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-taxonRectification.R:37:3): taxonRectification performs as expected ──
  testResult$`Searched Taxonomic Databases w/ Matches` == "NCBI" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 6 | WARN 22 | SKIP 15 | PASS 185 ]
  Error: Test failures
  Execution halted