Running 'testthat.R' [52s]
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 4 | WARN 0 | SKIP 17 | PASS 125 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (16)
  • internet connection established (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-studyTaxonList.R:17:3): studyTaxonList works with a phylogeny ───
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [resolver.globalnames.org] Connection timed out after 10013 milliseconds
  Backtrace:
       ▆
    1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-studyTaxonList.R:17:2
    2. │ └─base::isTRUE(condition)
    3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
    4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
    5.   ├─httr::http_error(HEAD(x, ...))
    6.   └─httr::HEAD(x, ...)
    7.     └─httr:::request_perform(req, hu$handle$handle)
    8.       ├─httr:::request_fetch(req$output, req$url, handle)
    9.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.         └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-studyTaxonList.R:52:3): studyTaxonList works with a vector of species ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [resolver.globalnames.org] Connection timed out after 10012 milliseconds
  Backtrace:
       ▆
    1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-studyTaxonList.R:52:2
    2. │ └─base::isTRUE(condition)
    3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
    4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
    5.   ├─httr::http_error(HEAD(x, ...))
    6.   └─httr::HEAD(x, ...)
    7.     └─httr:::request_perform(req, hu$handle$handle)
    8.       ├─httr:::request_fetch(req$output, req$url, handle)
    9.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.         └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-taxonRectification.R:7:3): functions on which it depends function as necessary ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [resolver.globalnames.org] Connection timed out after 10007 milliseconds
  Backtrace:
       ▆
    1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-taxonRectification.R:7:2
    2. │ └─base::isTRUE(condition)
    3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
    4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
    5.   ├─httr::http_error(HEAD(x, ...))
    6.   └─httr::HEAD(x, ...)
    7.     └─httr:::request_perform(req, hu$handle$handle)
    8.       ├─httr:::request_fetch(req$output, req$url, handle)
    9.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.         └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-taxonRectification.R:30:3): taxonRectification performs as expected ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [resolver.globalnames.org] Connection timed out after 10013 milliseconds
  Backtrace:
       ▆
    1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-taxonRectification.R:30:2
    2. │ └─base::isTRUE(condition)
    3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
    4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
    5.   ├─httr::http_error(HEAD(x, ...))
    6.   └─httr::HEAD(x, ...)
    7.     └─httr:::request_perform(req, hu$handle$handle)
    8.       ├─httr:::request_fetch(req$output, req$url, handle)
    9.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 4 | WARN 0 | SKIP 17 | PASS 125 ]
  Error: Test failures
  Execution halted