Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [51s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gwasrapidd)
  > 
  > test_check("gwasrapidd")
  [ FAIL 12 | WARN 2 | SKIP 1 | PASS 705 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-id_mapping.R:49:3): study_to_variant: warnings ──────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:49:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::study_to_variant(c("GCST0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_variants(study_id = .x, verbose = verbose, warnings = warnings)
   11.           └─gwasrapidd:::get_variants_by_study_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:75:3): study_to_trait: warnings ────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:75:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::study_to_trait(c("GCST0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_traits(study_id = .x, verbose = verbose, warnings = warnings)
   11.           └─gwasrapidd:::get_traits_by_study_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:101:3): association_to_study: warnings ─────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:101:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::association_to_study(c("0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_studies(...)
   11.           └─gwasrapidd:::get_studies_by_association_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:152:3): association_to_trait: warnings ─────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:152:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::association_to_trait(c("0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_traits(...)
   11.           └─gwasrapidd:::get_traits_by_association_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:178:3): variant_to_study: warnings ─────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:178:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::variant_to_study(c("rs0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_studies(variant_id = .x, verbose = verbose, warnings = warnings)
   11.           └─gwasrapidd:::get_studies_by_variant_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:204:3): variant_to_association: warnings ───────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:204:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::variant_to_association(c("rs0"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_associations(...)
   11.           └─gwasrapidd:::get_associations_by_variant_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:240:3): variant_to_trait: warnings ─────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:240:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::variant_to_trait(c("rs0"), warnings = TRUE)
    7.   └─gwasrapidd::variant_to_association(...)
    8.     └─purrr::map_dfr(...)
    9.       └─purrr::map(.x, .f, ...)
   10.         └─gwasrapidd (local) .f(.x[[i]], ...)
   11.           └─gwasrapidd::get_associations(...)
   12.             └─gwasrapidd:::get_associations_by_variant_id(...)
   13.               └─purrr::map(...)
   14.                 └─gwasrapidd (local) .f(.x[[i]], ...)
   15.                   └─gwasrapidd:::gc_request_all(...)
   16.                     └─gwasrapidd:::gc_request(...)
   17.                       └─httr::GET(url, user_agent_id)
   18.                         └─httr:::request_perform(req, hu$handle$handle)
   19.                           ├─httr:::request_fetch(req$output, req$url, handle)
   20.                           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   21.                             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:266:3): trait_to_study: warnings ───────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:266:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::trait_to_study(c("EFO_0000000"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_studies(efo_id = .x, verbose = verbose, warnings = warnings)
   11.           └─gwasrapidd:::get_studies_by_efo_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:292:3): trait_to_association: warnings ─────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:292:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::trait_to_association(c("EFO_0000000"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_associations(...)
   11.           └─gwasrapidd:::get_associations_by_efo_id(...)
   12.             └─purrr::map(...)
   13.               └─gwasrapidd (local) .f(.x[[i]], ...)
   14.                 └─gwasrapidd:::gc_request_all(...)
   15.                   └─gwasrapidd:::gc_request(...)
   16.                     └─httr::GET(url, user_agent_id)
   17.                       └─httr:::request_perform(req, hu$handle$handle)
   18.                         ├─httr:::request_fetch(req$output, req$url, handle)
   19.                         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   20.                           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-id_mapping.R:318:3): trait_to_variant: warnings ─────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-id_mapping.R:318:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd::trait_to_variant(c("EFO_0000000"), warnings = TRUE)
    7.   └─purrr::map_dfr(...)
    8.     └─purrr::map(.x, .f, ...)
    9.       └─gwasrapidd (local) .f(.x[[i]], ...)
   10.         └─gwasrapidd::get_variants(efo_id = .x, verbose = verbose, warnings = warnings)
   11.           └─gwasrapidd:::get_variants_by_efo_id(...)
   12.             └─gwasrapidd:::get_traits_by_efo_id(...)
   13.               └─purrr::map(...)
   14.                 └─gwasrapidd (local) .f(.x[[i]], ...)
   15.                   └─gwasrapidd:::gc_request_all(...)
   16.                     └─gwasrapidd:::gc_request(...)
   17.                       └─httr::GET(url, user_agent_id)
   18.                         └─httr:::request_perform(req, hu$handle$handle)
   19.                           ├─httr:::request_fetch(req$output, req$url, handle)
   20.                           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   21.                             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-request.R:8:3): gc_request: verbose flag ────────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_message(gc_request(verbose = TRUE)) at test-request.R:8:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd:::gc_request(verbose = TRUE)
    7.   └─httr::GET(url, user_agent_id)
    8.     └─httr:::request_perform(req, hu$handle$handle)
    9.       ├─httr:::request_fetch(req$output, req$url, handle)
   10.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11.         └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-request.R:14:3): gc_request: warnings flag ──────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: server certificate verification failed. CAfile: none CRLfile: none
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(gc_request(resource_url = "/foo", warnings = TRUE)) at test-request.R:14:2
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─gwasrapidd:::gc_request(resource_url = "/foo", warnings = TRUE)
    7.   └─httr::GET(url, user_agent_id)
    8.     └─httr:::request_perform(req, hu$handle$handle)
    9.       ├─httr:::request_fetch(req$output, req$url, handle)
   10.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 12 | WARN 2 | SKIP 1 | PASS 705 ]
  Error: Test failures
  Execution halted