Running ‘testthat.R’ [18s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  
   *** caught segfault ***
  address 0x5633cec4c4f8, cause 'invalid permissions'
  
  Traceback:
   1: curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
   2: crul_fetch(opts)
   3: private$make_request(rr)
   4: cli$get(query = args)
   5: taxize::gnr_resolve(names)
   6: func(unique_input, ...)
   7: map_unique(my_names, correct_taxon_names, database = database)
   8: lookup_funcs[[type]](query)
   9: lookup_tax_data("poa annus", type = "fuzzy_name")
  10: eval_bare(get_expr(quo), get_env(quo))
  11: quasi_label(enquo(object), label)
  12: expect_equal(lookup_tax_data("poa annus", type = "fuzzy_name")$taxon_names(),     lookup_tax_data("Poa annua", type = "taxon_name")$taxon_names())
  13: eval(code, test_env)
  14: eval(code, test_env)
  15: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  16: doTryCatch(return(expr), name, parentenv, handler)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  19: doTryCatch(return(expr), name, parentenv, handler)
  20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  21: tryCatchList(expr, classes, parentenv, handlers)
  22: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  23: test_code(desc, code, env = parent.frame())
  24: test_that("Taxmap can be intialized from queried data", {    raw_data <- data.frame(tax = c("Mammalia;Carnivora;Felidae",         "Mammalia;Carnivora;Felidae", "Mammalia;Carnivora;Ursidae"),         species = c("Panthera leo", "Panthera tigris", "Ursus americanus"),         my_tax_id = c("9689", "9694", "9643"), my_seq = c("AB548412",             "FJ358423", "DQ334818"), species_id = c("A", "B",             "C"))    abundance <- data.frame(id = c("A", "B", "C", "A", "B", "C"),         sample_id = c(1, 1, 1, 2, 2, 2), counts = c(23, 4, 3,             34, 5, 13))    common_names <- c(A = "Lion", B = "Tiger", C = "Bear", "Oh my!")    foods <- list(c("ungulates", "boar"), c("ungulates", "boar"),         c("salmon", "fruit", "nuts"))    name_result = lookup_tax_data(raw_data, type = "taxon_name",         datasets = list(counts = abundance, my_names = common_names,             foods = foods), mappings = c(species_id = "id", species_id = "{{name}}",             `{{index}}` = "{{index}}"), column = "species")    expect_equal(lookup_tax_data("poa annus", type = "fuzzy_name")$taxon_names(),         lookup_tax_data("Poa annua", type = "taxon_name")$taxon_names())    id_result = lookup_tax_data(raw_data, type = "taxon_id",         datasets = list(counts = abundance, my_names = common_names,             foods = foods), mappings = c(species_id = "id", species_id = "{{name}}",             `{{index}}` = "{{index}}"), column = "my_tax_id")    seq_result = lookup_tax_data(raw_data, type = "seq_id", datasets = list(counts = abundance,         my_names = common_names, foods = foods), mappings = c(species_id = "id",         species_id = "{{name}}", `{{index}}` = "{{index}}"),         column = "my_seq")    expect_equal(name_result, id_result)    expect_equal(name_result, seq_result)    expect_error(lookup_tax_data(1:3, type = "seq_id", database = "not valid"),         "not a valid database")    expect_error(lookup_tax_data(1:3, type = "seq_id", database = "bold"),         "not a valid database")    expect_error(lookup_tax_data(raw_data, column = "Not a column",         type = "seq_id"), "No column \"Not a column\" in input table")    expect_error(lookup_tax_data(raw_data, column = -1, type = "seq_id"),         "Column index \"-1\" out of bounds")    expect_error(lookup_tax_data(1:3, column = "Not a column",         type = "seq_id"), "No item named \"Not a column\" in the following inputs:")    expect_error(lookup_tax_data(1:3, column = 10, type = "seq_id"),         "out of bounds for inputs:")    raw_data <- data.frame(species = c("Panthera leo", "not a taxon",         "Ursus americanus"), my_tax_id = c("9689", "not a taxon id 6",         "9643"), my_seq = c("AB548412", "777777777777", "DQ334818"),         species_id = c("A", "B", "C"))    expect_warning(result <- lookup_tax_data(raw_data, type = "taxon_name",         column = "species"))    expect_warning(result <- lookup_tax_data(raw_data, type = "taxon_name",         column = "species"), ask = FALSE)    expect_equal(result$data$query_data$taxon_id[2], "unknown")    expect_warning(result <- lookup_tax_data(raw_data, type = "taxon_id",         column = "my_tax_id"))    expect_equal(result$data$query_data$taxon_id[2], "unknown")    expect_warning(result <- lookup_tax_data(raw_data, type = "seq_id",         column = "my_seq"))    expect_equal(result$data$query_data$taxon_id[2], "unknown")})
  25: eval(code, test_env)
  26: eval(code, test_env)
  27: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
  28: doTryCatch(return(expr), name, parentenv, handler)
  29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  31: doTryCatch(return(expr), name, parentenv, handler)
  32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
  33: tryCatchList(expr, classes, parentenv, handlers)
  34: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  35: test_code(NULL, exprs, env)
  36: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  37: force(code)
  38: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  39: FUN(X[[i]], ...)
  40: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  41: force(code)
  42: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  44: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  45: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  46: test_check("taxa")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault