Running ‘testthat.R’ [4s/158s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(queryup)
  > 
  > test_check("queryup")
  Query not supported
  Query not supported
  Query not supported
  Query not supported
  1 invalid values were found (CON_P22682) and removed from the query.
  Field 'accession_id' with no valid entries has been removed from query.
  Field 'accession' with no valid entries has been removed from query.
  Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%[ FAIL 14 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_uniprot_data.R:10'): Query with a single UniProt identifier works ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-get_uniprot_data.R:10:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─methods::is(get_uniprot_data("P22682")$content, "data.frame")
   5. └─queryup::get_uniprot_data("P22682")
   6.   └─jsonlite::fromJSON(RCurl::getURL(full_url))
   7.     └─jsonlite:::parse_and_simplify(...)
   8.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   9.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:16'): Call with no 'columns' defined works ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::get_uniprot_data(query, columns = NULL) at test-get_uniprot_data.R:16:2
   2.   └─jsonlite::fromJSON(RCurl::getURL(full_url))
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:23'): A message is returned if 'print_url' is TRUE ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test-get_uniprot_data.R:23:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─queryup::get_uniprot_data("P22682", print_url = TRUE)
    8.   └─jsonlite::fromJSON(RCurl::getURL(full_url))
    9.     └─jsonlite:::parse_and_simplify(...)
   10.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   11.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:27'): A message is returned if 'print_uniprot_messages' is TRUE ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test-get_uniprot_data.R:27:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─queryup::get_uniprot_data(...)
    8.   └─queryup::get_uniprot_data(...)
    9.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   10.       └─jsonlite:::parse_and_simplify(...)
   11.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   12.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:36'): Basic query works ─────────────────────
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::get_uniprot_data(query) at test-get_uniprot_data.R:36:2
   2.   └─jsonlite::fromJSON(RCurl::getURL(full_url))
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:63'): Query with only non valid entries works ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test-get_uniprot_data.R:63:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. ├─testthat::expect_message(get_uniprot_data(query), "invalid values were found")
    8. │ └─testthat:::expect_condition_matching(...)
    9. │   └─testthat:::quasi_capture(...)
   10. │     ├─testthat (local) .capture(...)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   13. └─queryup::get_uniprot_data(query)
   14.   └─queryup::get_uniprot_data(...)
   15.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   16.       └─jsonlite:::parse_and_simplify(...)
   17.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   18.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:74'): Query with non valid entries for multiple query fields works ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test-get_uniprot_data.R:74:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. ├─testthat::expect_message(get_uniprot_data(query), "invalid values were found")
    8. │ └─testthat:::expect_condition_matching(...)
    9. │   └─testthat:::quasi_capture(...)
   10. │     ├─testthat (local) .capture(...)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   13. └─queryup::get_uniprot_data(query)
   14.   └─queryup::get_uniprot_data(...)
   15.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   16.       └─jsonlite:::parse_and_simplify(...)
   17.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   18.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:85'): Query with valid and invalid values work ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_message(get_uniprot_data(query), "invalid values were found") at test-get_uniprot_data.R:85:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─queryup::get_uniprot_data(query)
    8.   └─queryup::get_uniprot_data(...)
    9.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   10.       └─jsonlite:::parse_and_simplify(...)
   11.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   12.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-get_uniprot_data.R:94'): Long queries work ─────────────────────
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-get_uniprot_data.R:94:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::setequal(get_uniprot_data(query)$content$Entry, ids)
    5. │ └─base::as.vector(x)
    6. └─queryup::get_uniprot_data(query)
    7.   └─jsonlite::fromJSON(RCurl::getURL(full_url))
    8.     └─jsonlite:::parse_and_simplify(...)
    9.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   10.         └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-query_uniprot.R:5'): Long queries work ─────────────────────────
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::query_uniprot(query) at test-query_uniprot.R:5:2
   2.   └─queryup::get_uniprot_data(...)
   3.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   4.       └─jsonlite:::parse_and_simplify(...)
   5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   6.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-query_uniprot.R:13'): Long queries with no columns defined work ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::query_uniprot(query, columns = NULL) at test-query_uniprot.R:13:2
   2.   └─queryup::get_uniprot_data(...)
   3.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   4.       └─jsonlite:::parse_and_simplify(...)
   5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   6.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-query_uniprot.R:22'): Short queries work ───────────────────────
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::query_uniprot(query) at test-query_uniprot.R:22:2
   2.   └─queryup::get_uniprot_data(query = query, columns = columns, print_url = print_url)
   3.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   4.       └─jsonlite:::parse_and_simplify(...)
   5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   6.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-query_uniprot.R:27'): Setting 'max_keys' above 300 produces a warning ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-query_uniprot.R:27:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─queryup::query_uniprot("P22682", max_keys = 301)
    8.   └─queryup::get_uniprot_data(query = query, columns = columns, print_url = print_url)
    9.     └─jsonlite::fromJSON(RCurl::getURL(full_url))
   10.       └─jsonlite:::parse_and_simplify(...)
   11.         └─jsonlite:::parseJSON(txt, bigint_as_char)
   12.           └─jsonlite:::parse_string(txt, bigint_as_char)
  ── Error ('test-query_uniprot.R:34'): Query works when multiple fields have more than 'max_keys' items ──
  Error: parse error: premature EOF
                                         
                       (right here) ------^
  
  Backtrace:
      ▆
   1. └─queryup::query_uniprot(...) at test-query_uniprot.R:34:2
   2.   └─base::lapply(...)
   3.     └─queryup (local) FUN(X[[i]], ...)
   4.       └─queryup::get_uniprot_data(...)
   5.         └─jsonlite::fromJSON(RCurl::getURL(full_url))
   6.           └─jsonlite:::parse_and_simplify(...)
   7.             └─jsonlite:::parseJSON(txt, bigint_as_char)
   8.               └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 14 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted