Running ‘test-all.R’ [1s/448s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  ── 1. Error: Get species works (@test_getspecies.R#2)  ─────────────────────────
  HTTP error 500.
  1: taxon_get_species("Vulpes") at testthat/test_getspecies.R:2
  2: jsonlite::fromJSON(paste(get_base_url(), "ts/all_species?taxon=", utils::URLencode(taxon), 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 2. Error: Get country species works (@test_getspecies.R#7)  ─────────────────
  HTTP error 500.
  1: taxon_get_species_and_country("Felidae", "Nepal") at testthat/test_getspecies.R:7
  2: jsonlite::fromJSON(paste(get_base_url(), "ts/country_species?taxon=", utils::URLencode(taxon), 
         "&country=", utils::URLencode(country), sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 3. Error: Get genome species works (@test_getspecies.R#13)  ─────────────────
  HTTP error 500.
  1: taxon_get_species_with_genome("Rodentia") at testthat/test_getspecies.R:13
  2: jsonlite::fromJSON(paste(get_base_url(), "ts/ncbi/genome_species?taxon=", utils::URLencode(taxon), 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 4. Error: Separating dark species works for OToL (@test_getspecies.R#19)  ───
  HTTP error 500.
  1: taxon_separate_dark_taxa_using_otol("vulpes") at testthat/test_getspecies.R:19
  2: unique(jsonlite::fromJSON(paste(get_base_url(), "ts/all_species?taxon=", utils::URLencode(taxon), 
         sep = ""))$species)
  3: jsonlite::fromJSON(paste(get_base_url(), "ts/all_species?taxon=", utils::URLencode(taxon), 
         sep = ""))
  4: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  5: parseJSON(txt, bigint_as_char)
  6: parse_con(txt, bigint_as_char)
  7: open(con, "rb")
  8: open.connection(con, "rb")
  
  ── 5. Error: Separating dark species works for NCBI (@test_getspecies.R#28)  ───
  HTTP error 500.
  1: taxon_separate_dark_taxa_using_otol("Poa") at testthat/test_getspecies.R:28
  2: unique(jsonlite::fromJSON(paste(get_base_url(), "ts/all_species?taxon=", utils::URLencode(taxon), 
         sep = ""))$species)
  3: jsonlite::fromJSON(paste(get_base_url(), "ts/all_species?taxon=", utils::URLencode(taxon), 
         sep = ""))
  4: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  5: parseJSON(txt, bigint_as_char)
  6: parse_con(txt, bigint_as_char)
  7: open(con, "rb")
  8: open.connection(con, "rb")
  
  ── 6. Error: Loading names from a standard web page works correctly (@test_names
  HTTP error 500.
  1: url_get_scientific_names("http://en.wikipedia.org/wiki/Ant") at testthat/test_names.R:2
  2: jsonlite::fromJSON(paste(get_base_url(), "fn/names_url?url=", URL, "&engine=", search_engine, 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 7. Error: Loading names from an online PDF works correctly (@test_names.R#8) 
  HTTP error 500.
  1: url_get_scientific_names("https://www.fws.gov/westvirginiafieldoffice/PDF/beechridgehcp/Appendix_D_Table_D-1.pdf") at testthat/test_names.R:8
  2: jsonlite::fromJSON(paste(get_base_url(), "fn/names_url?url=", URL, "&engine=", search_engine, 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 8. Error: Loading names from a text string works correctly (@test_names.R#15)
  HTTP error 500.
  1: text_get_scientific_names("Formica polyctena is a species of European red wood ant in the genus Formica. The pavement ant, Tetramorium caespitum is an ant native to Europe. Pseudomyrmex is a genus of stinging, wasp-like ants. Adetomyrma venatrix is an endangered species of ants endemic to Madagascar. Carebara diversa is a species of ants in the subfamily Formicinae. It is found in many Asian countries.") at testthat/test_names.R:15
  2: jsonlite::fromJSON((paste(get_base_url(), "fn/names_text?text=", utils::URLencode(gsub("[^[:alnum:] ]", 
         "", as.character(text))), "&engine=", search_engine, sep = "")))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 9. Error: Resolving names with OToL works (@test_names.R#22)  ───────────────
  HTTP error 500.
  1: expect_warning(taxa.new <- taxa_resolve_names_with_otol(taxa)) at testthat/test_names.R:22
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: taxa_resolve_names_with_otol(taxa)
  7: jsonlite::fromJSON(paste(get_base_url(), "tnrs/ot/resolve?names=", taxa.string, sep = ""))
  8: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  9: parseJSON(txt, bigint_as_char)
  10: parse_con(txt, bigint_as_char)
  11: open(con, "rb")
  12: open.connection(con, "rb")
  
  ── 10. Error: Resolving names with GNR works (@test_resolver.R#3)  ─────────────
  HTTP error 500.
  1: expect_gte(length(taxa.new <- taxa_resolve_names_with_gnr(taxa)), 3) at testthat/test_resolver.R:3
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: taxa_resolve_names_with_gnr(taxa)
  5: jsonlite::fromJSON(paste(get_base_url(), "tnrs/gnr/resolve?names=", taxa.string, 
         sep = ""))
  6: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  7: parseJSON(txt, bigint_as_char)
  8: parse_con(txt, bigint_as_char)
  9: open(con, "rb")
  10: open.connection(con, "rb")
  
  ── 11. Error: Get species info works (@test_speciesinfo.R#2)  ──────────────────
  HTTP error 500.
  1: species_get_info(c("Myrmecocystus mexicanus")) at testthat/test_speciesinfo.R:2
  2: jsonlite::fromJSON(paste(get_base_url(), "sl/eol/get_links?species=", utils::URLencode(spec.string), 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 12. Error: Get image metadata of species works (@test_speciesinfo.R#8)  ─────
  HTTP error 500.
  1: species_get_image_data(c("Myrmecocystus mexicanus")) at testthat/test_speciesinfo.R:8
  2: jsonlite::fromJSON(paste(get_base_url(), "si/eol/get_images?species=", utils::URLencode(spec.string), 
         sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 13. Error: Loading a tree from OToL (@test_tree.R#3)  ───────────────────────
  HTTP error 500.
  1: taxa_get_otol_tree(taxa) at testthat/test_tree.R:3
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/ot/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 14. Error: Loading a tree from Phylomatic (@test_tree.R#10)  ────────────────
  HTTP error 500.
  1: taxa_get_phylomatic_tree(taxa) at testthat/test_tree.R:10
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pm/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ── 15. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  ─────────────
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 15
  1. Error: Get species works (@test_getspecies.R#2) 
  2. Error: Get country species works (@test_getspecies.R#7) 
  3. Error: Get genome species works (@test_getspecies.R#13) 
  4. Error: Separating dark species works for OToL (@test_getspecies.R#19) 
  5. Error: Separating dark species works for NCBI (@test_getspecies.R#28) 
  6. Error: Loading names from a standard web page works correctly (@test_names.R#2) 
  7. Error: Loading names from an online PDF works correctly (@test_names.R#8) 
  8. Error: Loading names from a text string works correctly (@test_names.R#15) 
  9. Error: Resolving names with OToL works (@test_names.R#22) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted