Running ‘testthat.R’ [111s/213s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(galah)
  
  Attaching package: 'galah'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > galah_config(cache_directory = tempdir(), email = "ala4r@ala.org.au",
  +            caching = FALSE, atlas = "Australia", verbose = FALSE,
  +            run_checks = TRUE)
  > test_check("galah")
  [ FAIL 14 | WARN 72 | SKIP 92 | PASS 520 ]
  
  ══ Skipped tests (92) ══════════════════════════════════════════════════════════
  • On CRAN (92): 'test-atlas_media.R:5:3', 'test-atlas_media.R:20:3',
    'test-atlas_media.R:35:3', 'test-atlas_occurrences.R:9:3',
    'test-atlas_occurrences.R:24:3', 'test-atlas_occurrences.R:45:3',
    'test-atlas_occurrences.R:78:3', 'test-atlas_species.R:11:3',
    'test-atlas_species.R:25:3', 'test-atlas_species.R:42:3',
    'test-clear_cached_files.R:4:3', 'test-collect_media.R:2:3',
    'test-collect_media.R:13:3', 'test-collect_media.R:21:3',
    'test-collect_media.R:54:3', 'test-collect_occurrences.R:2:3',
    'test-deprecated_functions.R:46:3', 'test-deprecated_functions.R:59:3',
    'test-deprecated_functions.R:76:3', 'test-deprecated_functions.R:81:3',
    'test-deprecated_functions.R:87:3', 'test-deprecated_functions.R:93:3',
    'test-deprecated_functions.R:100:3', 'test-deprecated_functions.R:107:3',
    'test-deprecated_functions.R:127:3', 'test-deprecated_functions.R:132:3',
    'test-deprecated_functions.R:138:3', 'test-deprecated_functions.R:143:3',
    'test-deprecated_functions.R:149:3', 'test-deprecated_functions.R:154:3',
    'test-deprecated_functions.R:160:3', 'test-deprecated_functions.R:165:3',
    'test-galah_apply_profile.R:18:3', 'test-galah_apply_profile.R:35:3',
    'test-galah_config.R:4:3', 'test-galah_polygon.R:21:3',
    'test-galah_select.R:12:3', 'test-galah_select.R:24:3',
    'test-galah_select.R:96:3', 'test-galah_select.R:103:3',
    'test-international-Austria.R:138:3', 'test-international-Brazil.R:135:3',
    'test-international-France.R:98:5', 'test-international-France.R:115:5',
    'test-international-France.R:127:3', 'test-international-France.R:139:3',
    'test-international-GBIF.R:159:3', 'test-international-Guatemala.R:126:3',
    'test-international-Sweden.R:117:5', 'test-international-Sweden.R:128:3',
    'test-search_all.R:4:3', 'test-search_all.R:9:3', 'test-search_all.R:29:3',
    'test-search_all.R:35:3', 'test-search_all.R:49:3', 'test-search_all.R:62:3',
    'test-search_all.R:75:3', 'test-search_all.R:88:3',
    'test-search_all.R:101:3', 'test-search_all.R:115:3',
    'test-search_all.R:128:3', 'test-search_all.R:134:3',
    'test-search_all.R:147:3', 'test-search_all.R:160:3',
    'test-search_all.R:174:3', 'test-search_all.R:187:3', 'test-show_all.R:5:3',
    'test-show_all.R:31:3', 'test-show_all.R:39:3', 'test-show_all.R:47:3',
    'test-show_all.R:55:3', 'test-show_all.R:63:3', 'test-show_all.R:71:3',
    'test-show_all.R:79:3', 'test-show_all.R:87:3', 'test-show_all.R:95:3',
    'test-show_all.R:103:3', 'test-show_all.R:111:3',
    'test-show_all_cached_files.R:4:3', 'test-show_values.R:18:3',
    'test-show_values.R:28:3', 'test-show_values.R:42:3',
    'test-show_values.R:56:3', 'test-show_values.R:70:3',
    'test-show_values.R:76:3', 'test-show_values.R:91:3',
    'test-show_values.R:106:3', 'test-show_values.R:122:3',
    'test-show_values.R:131:3', 'test-show_values.R:145:3',
    'test-show_values.R:164:3', 'test-show_values.R:183:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-deprecated_functions.R:14:3'): select_columns is deprecated ────
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `FUN(X[[i]], ...)`: Can't subset columns that don't exist.
  ✖ Column `eventDate` doesn't exist.
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(select_columns(eventDate)) at test-deprecated_functions.R:14:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─galah::select_columns(eventDate)
    7. │ └─galah::galah_select(..., group = group)
    8. │   └─galah:::parse_select(dots, group_chosen)
    9. │     ├─base::unlist(...)
   10. │     └─base::lapply(...)
   11. │       └─galah (local) FUN(X[[i]], ...)
   12. │         └─tidyselect::eval_select(a, data = df)
   13. │           └─tidyselect:::eval_select_impl(...)
   14. │             ├─tidyselect:::with_subscript_errors(...)
   15. │             │ └─rlang::try_fetch(...)
   16. │             │   └─base::withCallingHandlers(...)
   17. │             └─tidyselect:::vars_select_eval(...)
   18. │               └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   19. │                 └─tidyselect:::as_indices_sel_impl(...)
   20. │                   └─tidyselect:::as_indices_impl(...)
   21. │                     └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   22. │                       └─vctrs::vec_as_location(...)
   23. └─vctrs (local) `<fn>`()
   24.   └─vctrs:::stop_subscript_oob(...)
   25.     └─vctrs:::stop_subscript(...)
   26.       └─rlang::abort(...)
  ── Error ('test-deprecated_functions.R:18:3'): select_columns works ────────────
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `FUN(X[[i]], ...)`: Can't subset columns that don't exist.
  ✖ Column `eventDate` doesn't exist.
  Backtrace:
       ▆
    1. ├─galah::select_columns(eventDate) at test-deprecated_functions.R:18:3
    2. │ └─galah::galah_select(..., group = group)
    3. │   └─galah:::parse_select(dots, group_chosen)
    4. │     ├─base::unlist(...)
    5. │     └─base::lapply(...)
    6. │       └─galah (local) FUN(X[[i]], ...)
    7. │         └─tidyselect::eval_select(a, data = df)
    8. │           └─tidyselect:::eval_select_impl(...)
    9. │             ├─tidyselect:::with_subscript_errors(...)
   10. │             │ └─rlang::try_fetch(...)
   11. │             │   └─base::withCallingHandlers(...)
   12. │             └─tidyselect:::vars_select_eval(...)
   13. │               └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   14. │                 └─tidyselect:::as_indices_sel_impl(...)
   15. │                   └─tidyselect:::as_indices_impl(...)
   16. │                     └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   17. │                       └─vctrs::vec_as_location(...)
   18. └─vctrs (local) `<fn>`()
   19.   └─vctrs:::stop_subscript_oob(...)
   20.     └─vctrs:::stop_subscript(...)
   21.       └─rlang::abort(...)
  ── Error ('test-galah_call.R:11:3'): galah_call works with all `galah_` functions ──
  Error in `eval(code, test_env)`: Can't provide tree more than one taxonomic rank to end with.
  ℹ galah_down_to` only accepts a single rank at a time.
  ✖ `galah_down_to` has length of 2.
  Backtrace:
      ▆
   1. └─galah::galah_down_to(...) at test-galah_call.R:11:3
   2.   └─rlang::abort(bullets, call = caller_env())
  ── Error ('test-galah_call.R:23:3'): galah_call works irrespective of `galah_` function order ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `FUN(X[[i]], ...)`: Can't subset columns that don't exist.
  ✖ Column `year` doesn't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_identify(...) at test-galah_call.R:23:3
    2. │ └─galah:::parse_identify(dots, search)
    3. │   └─galah:::parse_basic_quosures(dots)
    4. │     └─base::lapply(dots[is_either], eval_tidy)
    5. │       └─rlang (local) FUN(X[[i]], ...)
    6. ├─galah::galah_filter(...)
    7. │ └─galah:::parse_filter(dots)
    8. │   └─galah:::parse_objects_or_functions(dots)
    9. │     └─base::lapply(...)
   10. │       └─galah (local) FUN(X[[i]], ...)
   11. │         ├─galah:::serialise_quosure(eval_tidy(a))
   12. │         └─rlang::eval_tidy(a)
   13. ├─galah::galah_select(...)
   14. │ └─galah:::parse_select(dots, group_chosen)
   15. │   ├─base::unlist(...)
   16. │   └─base::lapply(...)
   17. │     └─galah (local) FUN(X[[i]], ...)
   18. │       └─tidyselect::eval_select(a, data = df)
   19. │         └─tidyselect:::eval_select_impl(...)
   20. │           ├─tidyselect:::with_subscript_errors(...)
   21. │           │ └─rlang::try_fetch(...)
   22. │           │   └─base::withCallingHandlers(...)
   23. │           └─tidyselect:::vars_select_eval(...)
   24. │             └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   25. │               └─tidyselect:::as_indices_sel_impl(...)
   26. │                 └─tidyselect:::as_indices_impl(...)
   27. │                   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   28. │                     └─vctrs::vec_as_location(...)
   29. └─vctrs (local) `<fn>`()
   30.   └─vctrs:::stop_subscript_oob(...)
   31.     └─vctrs:::stop_subscript(...)
   32.       └─rlang::abort(...)
  ── Failure ('test-galah_filter.R:35:3'): galah_filter handles assertion filters ──
  grepl("assertions", filters$query) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-galah_filter.R:48:3'): galah_filter skips checks if requested ──
  `galah_filter(random == "filter")` produced messages.
  ── Error ('test-galah_select.R:35:3'): galah_select builds expected columns when group = basic ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `decimalLatitude`, `decimalLongitude`, `eventDate`, `scientificName`, `taxonConceptID`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_select(group = "basic") at test-galah_select.R:35:3
    2. │ └─galah:::parse_select(dots, group_chosen)
    3. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    4. │   │ ├─tidyselect:::eval_select_impl(...)
    5. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    6. │   │ │ │ └─rlang::try_fetch(...)
    7. │   │ │ │   └─base::withCallingHandlers(...)
    8. │   │ │ └─tidyselect:::vars_select_eval(...)
    9. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   10. │   │ │     └─rlang::is_quosure(x)
   11. │   │ └─rlang::as_quosure(expr, env)
   12. │   │   └─rlang::is_quosure(x)
   13. │   └─tidyselect::all_of(group_cols)
   14. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   15. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   16. │         └─vctrs::vec_as_location(...)
   17. └─vctrs (local) `<fn>`()
   18.   └─vctrs:::stop_subscript_oob(...)
   19.     └─vctrs:::stop_subscript(...)
   20.       └─rlang::abort(...)
  ── Error ('test-galah_select.R:52:3'): galah_select builds expected columns when group = event ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `eventRemarks`, `eventTime`, `eventID`, `eventDate`, `samplingEffort`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_select(group = "event") at test-galah_select.R:52:3
    2. │ └─galah:::parse_select(dots, group_chosen)
    3. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    4. │   │ ├─tidyselect:::eval_select_impl(...)
    5. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    6. │   │ │ │ └─rlang::try_fetch(...)
    7. │   │ │ │   └─base::withCallingHandlers(...)
    8. │   │ │ └─tidyselect:::vars_select_eval(...)
    9. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   10. │   │ │     └─rlang::is_quosure(x)
   11. │   │ └─rlang::as_quosure(expr, env)
   12. │   │   └─rlang::is_quosure(x)
   13. │   └─tidyselect::all_of(group_cols)
   14. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   15. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   16. │         └─vctrs::vec_as_location(...)
   17. └─vctrs (local) `<fn>`()
   18.   └─vctrs:::stop_subscript_oob(...)
   19.     └─vctrs:::stop_subscript(...)
   20.       └─rlang::abort(...)
  ── Error ('test-galah_select.R:70:3'): galah_select accepts multiple groups ────
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `decimalLatitude`, `decimalLongitude`, `eventDate`, `scientificName`, `taxonConceptID`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_select(group = c("basic", "assertions")) at test-galah_select.R:70:3
    2. │ └─galah:::parse_select(dots, group_chosen)
    3. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    4. │   │ ├─tidyselect:::eval_select_impl(...)
    5. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    6. │   │ │ │ └─rlang::try_fetch(...)
    7. │   │ │ │   └─base::withCallingHandlers(...)
    8. │   │ │ └─tidyselect:::vars_select_eval(...)
    9. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   10. │   │ │     └─rlang::is_quosure(x)
   11. │   │ └─rlang::as_quosure(expr, env)
   12. │   │   └─rlang::is_quosure(x)
   13. │   └─tidyselect::all_of(group_cols)
   14. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   15. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   16. │         └─vctrs::vec_as_location(...)
   17. └─vctrs (local) `<fn>`()
   18.   └─vctrs:::stop_subscript_oob(...)
   19.     └─vctrs:::stop_subscript(...)
   20.       └─rlang::abort(...)
  ── Error ('test-galah_select.R:88:3'): galah_select defaults to group = basic when there are no args ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `decimalLatitude`, `decimalLongitude`, `eventDate`, `scientificName`, `taxonConceptID`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(galah_select(), "data.frame") at test-galah_select.R:88:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─galah::galah_select()
    5. │ └─galah:::parse_select(dots, group_chosen)
    6. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    7. │   │ ├─tidyselect:::eval_select_impl(...)
    8. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    9. │   │ │ │ └─rlang::try_fetch(...)
   10. │   │ │ │   └─base::withCallingHandlers(...)
   11. │   │ │ └─tidyselect:::vars_select_eval(...)
   12. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   13. │   │ │     └─rlang::is_quosure(x)
   14. │   │ └─rlang::as_quosure(expr, env)
   15. │   │   └─rlang::is_quosure(x)
   16. │   └─tidyselect::all_of(group_cols)
   17. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   18. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   19. │         └─vctrs::vec_as_location(...)
   20. └─vctrs (local) `<fn>`()
   21.   └─vctrs:::stop_subscript_oob(...)
   22.     └─vctrs:::stop_subscript(...)
   23.       └─rlang::abort(...)
  ── Error ('test-galah_select.R:136:3'): galah_select can use tidyselect::last_col & user-defined queries ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `FUN(X[[i]], ...)`: Can't subset columns that don't exist.
  ✖ Column `year` doesn't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_select(year, basisOfRecord, tidyselect::last_col()) at test-galah_select.R:136:3
    2. │ └─galah:::parse_select(dots, group_chosen)
    3. │   ├─base::unlist(...)
    4. │   └─base::lapply(...)
    5. │     └─galah (local) FUN(X[[i]], ...)
    6. │       └─tidyselect::eval_select(a, data = df)
    7. │         └─tidyselect:::eval_select_impl(...)
    8. │           ├─tidyselect:::with_subscript_errors(...)
    9. │           │ └─rlang::try_fetch(...)
   10. │           │   └─base::withCallingHandlers(...)
   11. │           └─tidyselect:::vars_select_eval(...)
   12. │             └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   13. │               └─tidyselect:::as_indices_sel_impl(...)
   14. │                 └─tidyselect:::as_indices_impl(...)
   15. │                   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   16. │                     └─vctrs::vec_as_location(...)
   17. └─vctrs (local) `<fn>`()
   18.   └─vctrs:::stop_subscript_oob(...)
   19.     └─vctrs:::stop_subscript(...)
   20.       └─rlang::abort(...)
  ── Error ('test-galah_select.R:141:3'): galah_select can use tidyselect::last_col & group ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `decimalLatitude`, `decimalLongitude`, `eventDate`, `scientificName`, `taxonConceptID`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─galah::galah_select(tidyselect::last_col(), group = "basic") at test-galah_select.R:141:3
    2. │ └─galah:::parse_select(dots, group_chosen)
    3. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    4. │   │ ├─tidyselect:::eval_select_impl(...)
    5. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    6. │   │ │ │ └─rlang::try_fetch(...)
    7. │   │ │ │   └─base::withCallingHandlers(...)
    8. │   │ │ └─tidyselect:::vars_select_eval(...)
    9. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   10. │   │ │     └─rlang::is_quosure(x)
   11. │   │ └─rlang::as_quosure(expr, env)
   12. │   │   └─rlang::is_quosure(x)
   13. │   └─tidyselect::all_of(group_cols)
   14. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   15. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   16. │         └─vctrs::vec_as_location(...)
   17. └─vctrs (local) `<fn>`()
   18.   └─vctrs:::stop_subscript_oob(...)
   19.     └─vctrs:::stop_subscript(...)
   20.       └─rlang::abort(...)
  ── Error ('test-masked-functions.R:18:3'): `select` works identically to piped `galah_select` ──
  <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
  Error in `all_of(group_cols)`: Can't subset columns that don't exist.
  ✖ Columns `decimalLatitude`, `decimalLongitude`, `eventDate`, `scientificName`, `taxonConceptID`, etc. don't exist.
  Backtrace:
       ▆
    1. ├─dplyr::select(galah_call(), year, group = "basic") at test-masked-functions.R:18:3
    2. ├─galah:::select.data_request(galah_call(), year, group = "basic")
    3. │ ├─galah:::update_galah_call(...)
    4. │ └─galah:::parse_select(dots, group_chosen)
    5. │   ├─tidyselect::eval_select(all_of(group_cols), data = df)
    6. │   │ ├─tidyselect:::eval_select_impl(...)
    7. │   │ │ ├─tidyselect:::with_subscript_errors(...)
    8. │   │ │ │ └─rlang::try_fetch(...)
    9. │   │ │ │   └─base::withCallingHandlers(...)
   10. │   │ │ └─tidyselect:::vars_select_eval(...)
   11. │   │ │   └─tidyselect:::quo_get_expr2(expr, expr)
   12. │   │ │     └─rlang::is_quosure(x)
   13. │   │ └─rlang::as_quosure(expr, env)
   14. │   │   └─rlang::is_quosure(x)
   15. │   └─tidyselect::all_of(group_cols)
   16. │     └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
   17. │       └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
   18. │         └─vctrs::vec_as_location(...)
   19. └─vctrs (local) `<fn>`()
   20.   └─vctrs:::stop_subscript_oob(...)
   21.     └─vctrs:::stop_subscript(...)
   22.       └─rlang::abort(...)
  ── Failure ('test-masked-functions.R:52:3'): `slice_head` works for atlas_counts ──
  nrow(result) not equal to 5.
  1/1 mismatches
  [1] 0 - 5 == -5
  
  [ FAIL 14 | WARN 72 | SKIP 92 | PASS 520 ]
  Error: Test failures
  Execution halted