Running 'testthat.R' [5s]
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
  Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%Querying the UniProt database...
  
    |                                                                            
    |                                                                      |   0%[ FAIL 15 | WARN 0 | SKIP 0 | PASS 5 ]
  
  == Failed tests ================================================================
  -- Error (test-get_uniprot_data.R:10:3): Query with a single UniProt identifier works --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   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. | \-RCurl::getURL(full_url)
   8. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   9. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:16:3): Call with no 'columns' defined works --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   1. +-queryup::get_uniprot_data(query, columns = NULL) at test-get_uniprot_data.R:16:2
   2. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
   3. | \-RCurl::getURL(full_url)
   4. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   5. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:23:3): A message is returned if 'print_url' is TRUE --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    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. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:27:3): A message is returned if 'print_uniprot_messages' is TRUE --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
    9. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:36:3): Basic query works ---------------------
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   1. +-queryup::get_uniprot_data(query) at test-get_uniprot_data.R:36:2
   2. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
   3. | \-RCurl::getURL(full_url)
   4. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   5. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:47:3): Query with unrecognized query fields fails with a warning --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    1. +-testthat::expect_warning(get_uniprot_data(query), "request failed") at test-get_uniprot_data.R:47:2
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
    9. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:55:3): Query with unrecognized field parameter fails with a warning --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    1. +-testthat::expect_warning(...) at test-get_uniprot_data.R:55:2
    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, columns = columns)
    8. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
    9. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:63:3): Query with only non valid entries works --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
   15. | \-RCurl::getURL(full_url)
   16. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   17. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:74:3): Query with non valid entries for multiple query fields works --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
   15. | \-RCurl::getURL(full_url)
   16. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   17. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:85:3): Query with valid and invalid values work --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
    9. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-get_uniprot_data.R:94:3): Long queries fail with a warning ------
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
       x
    1. +-testthat::expect_warning(get_uniprot_data(query), "request failed") at test-get_uniprot_data.R:94:2
    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. | +-jsonlite::fromJSON(RCurl::getURL(full_url))
    9. | \-RCurl::getURL(full_url)
   10. |   \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   11. \-RCurl (local) `<fn>`(...)
  -- Error (test-query_uniprot.R:5:3): Long queries work -------------------------
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   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. |   \-RCurl::getURL(full_url)
   5. |     \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   6. \-RCurl (local) `<fn>`(...)
  -- Error (test-query_uniprot.R:13:3): Long queries with no columns defined work --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   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. |   \-RCurl::getURL(full_url)
   5. |     \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   6. \-RCurl (local) `<fn>`(...)
  -- Error (test-query_uniprot.R:22:3): Short queries work -----------------------
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   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. |   \-RCurl::getURL(full_url)
   5. |     \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   6. \-RCurl (local) `<fn>`(...)
  -- Error (test-query_uniprot.R:34:3): Query works when multiple fields have more than 'max_keys' items --
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol", 
      TRUE)`: error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol
  Backtrace:
      x
   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. |       \-RCurl::getURL(full_url)
   7. |         \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   8. \-RCurl (local) `<fn>`(...)
  
  [ FAIL 15 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted