Running ‘testthat.R’ [7s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(occCite)
  > 
  > test_check("occCite")
  [1] "NOTE: 1 BIEN dataset(s) for Protea cynaroides is/are missing citation data. Key(s) missing citations are: 280. Source(s) are identified as: MO."
  	
   OccCite query occurred on: 24 November, 2020
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: NCBI
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name        Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides                           NCBI
  	
   Sources for occurrence data: gbif, bien
   	
              Species Occurrences Sources
  1 Protea cynaroides        1293      17
  	
   GBIF dataset DOIs: 	
  
              Species GBIF Access Date           GBIF DOI
  1 Protea cynaroides       2020-11-23 10.15468/dl.2449qy
  	
   OccCite query occurred on: 24 November, 2020
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: NCBI
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name        Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides                           NCBI
  	
   Sources for occurrence data: gbif
   	
              Species Occurrences Sources
  1 Protea cynaroides        1145      12
  	
   GBIF dataset DOIs: 	
  
              Species GBIF Access Date           GBIF DOI
  1 Protea cynaroides       2020-11-23 10.15468/dl.2449qy
  	
   OccCite query occurred on: 24 November, 2020
  	
   User query type: User-supplied list of taxa.
  	
   Sources for taxonomic rectification: NCBI
   	
  	
   Taxonomic cleaning results: 	
  
           Input Name        Best Match Taxonomic Databases w/ Matches
  1 Protea cynaroides Protea cynaroides                           NCBI
  	
   Sources for occurrence data: bien
   	
              Species Occurrences Sources
  1 Protea cynaroides         148       5
  [ FAIL 9 | WARN 0 | SKIP 19 | PASS 129 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (16)
  • httr::http_error("https://resolver.globalnames.org/data_sources.json") is TRUE (2)
  • internet connection established (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-studyTaxonList.R:26:3): studyTaxonList works with a phylogeny ──
  class(testResult) == "occCiteData" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:27:3): studyTaxonList works with a phylogeny ──
  "userQueryType" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:28:3): studyTaxonList works with a phylogeny ──
  "userSpecTaxonomy" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:29:3): studyTaxonList works with a phylogeny ──
  "cleanedTaxonomy" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:30:3): studyTaxonList works with a phylogeny ──
  "occSources" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:31:3): studyTaxonList works with a phylogeny ──
  "occCiteSearchDate" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-studyTaxonList.R:32:3): studyTaxonList works with a phylogeny ──
  "occResults" %in% slotNames(testResult) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error (test-studyTaxonList.R:34:3): studyTaxonList works with a phylogeny ───
  Error in `eval_bare(expr, quo_get_env(quo))`: trying to get slot "userQueryType" from an object of a basic class ("NULL") with no slots
  Backtrace:
      ▆
   1. └─testthat::expect_true(testResult@userQueryType == "User-supplied phylogeny.") at test-studyTaxonList.R:34:2
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Error (test-taxonRectification.R:17:3): functions on which it depends function as necessary ──
  Error: Service Unavailable (HTTP 503)
  Backtrace:
      ▆
   1. └─taxize::gnr_resolve(sci = "Buteo buteo", data_source_ids = sourceIDs) at test-taxonRectification.R:17:2
   2.   └─tmp$raise_for_status()
  
  [ FAIL 9 | WARN 0 | SKIP 19 | PASS 129 ]
  Error: Test failures
  Execution halted