Last updated on 2025-07-21 09:50:25 CEST.
| Package | ERROR | OK |
|---|---|---|
| rgbif | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
Version: 3.8.2
Check: tests
Result: ERROR
Running ‘test-all.R’ [43s/88s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("rgbif")
Loading required package: rgbif
[ FAIL 7 | WARN 2 | SKIP 137 | PASS 1271 ]
══ Skipped tests (137) ═════════════════════════════════════════════════════════
• On CRAN (137): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1',
'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:19:3',
'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3',
'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3',
'test-derived_dataset.R:347:3', 'test-downloads.R:3:3',
'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3',
'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3',
'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3',
'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3',
'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5',
'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3',
'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3',
'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5',
'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3',
'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3',
'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3',
'test-name_backbone_checklist.R:273:3',
'test-name_backbone_checklist.R:368:3',
'test-name_backbone_checklist.R:466:3',
'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3',
'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3',
'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3',
'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5',
'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3',
'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3',
'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3',
'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3',
'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3',
'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3',
'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3',
'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3',
'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3',
'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3',
'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3',
'test-occ_download_cancel.R:27:3',
'test-occ_download_dataset_activity.R:4:3',
'test-occ_download_dataset_activity.R:26:3',
'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3',
'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3',
'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3',
'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3',
'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3',
'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3',
'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3',
'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3',
'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3',
'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3',
'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3',
'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3',
'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3',
'test-occ_search.r:101:3', 'test-occ_search.r:114:3',
'test-occ_search.r:128:3', 'test-occ_search.r:143:3',
'test-occ_search.r:161:3', 'test-occ_search.r:178:3',
'test-occ_search.r:195:3', 'test-occ_search.r:214:3',
'test-occ_search.r:231:3', 'test-occ_search.r:248:3',
'test-occ_search.r:266:3', 'test-occ_search.r:283:3',
'test-occ_search.r:300:3', 'test-occ_search.r:318:3',
'test-occ_search.r:336:3', 'test-occ_search.r:354:3',
'test-occ_search.r:369:3', 'test-occ_search.r:386:3',
'test-occ_search.r:436:3', 'test-occ_search.r:510:3',
'test-organizations.r:4:3', 'test-organizations.r:67:3',
'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3',
'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-oai.R:5:5'): gbif_oai_identify ─────────────────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-clang/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:4:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_identify() at test-oai.R:5:5
4. ├─base::as.list(oai::id(url = gboai(), ...))
5. └─oai::id(url = gboai(), ...)
6. ├─plyr::rbind.fill(lapply(url, id_, as = as, ...))
7. └─base::lapply(url, id_, as = as, ...)
8. └─oai (local) FUN(X[[i]], ...)
9. ├─oai:::get_headers(xml_children(xml2::read_xml(tt))[[3]])
10. │ ├─base::lapply(...)
11. │ └─xml2::xml_children(m)
12. │ └─xml2:::nodeset_apply(x, function(x) .Call(node_children, x, TRUE))
13. ├─xml2::xml_children(xml2::read_xml(tt))
14. │ └─xml2:::nodeset_apply(x, function(x) .Call(node_children, x, TRUE))
15. ├─xml2::read_xml(tt)
16. └─xml2:::read_xml.character(tt)
17. └─xml2:::path_to_connection(x)
18. └─xml2:::check_path(path)
19. └─cli::cli_abort(msg, call = call)
20. └─rlang::abort(...)
── Error ('test-oai.R:15:5'): gbif_oai_list_metadataformats ────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-clang/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:14:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_metadataformats() at test-oai.R:15:5
4. └─oai::list_metadataformats(url = gboai(), id = id, ...)
5. └─oai:::one_mf(id, url, ...)
6. ├─xml2::read_xml(out)
7. └─xml2:::read_xml.character(out)
8. └─xml2:::path_to_connection(x)
9. └─xml2:::check_path(path)
10. └─cli::cli_abort(msg, call = call)
11. └─rlang::abort(...)
── Error ('test-oai.R:25:5'): gbif_oai_list_sets ───────────────────────────────
Error in `while_oai(url, args, token, as, ...)`: cannot parse downloaded XML, dumped raw XML to file ./oaidump_2025-07-21_07-35-48.4185921592dc361a8375xml
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:24:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_sets() at test-oai.R:25:5
4. └─oai::list_sets(url = gboai(), token = token, as = as, ...)
5. └─oai:::while_oai(url, args, token, as, ...)
── Error ('test-oai.R:37:5'): gbif_oai_list_identifiers ────────────────────────
Error in `while_oai(url, args, token, as, ...)`: cannot parse downloaded XML, dumped raw XML to file ./oaidump_2025-07-21_07-35-48.9496831592dc5cc60577xml
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:35:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_identifiers(from = "2019-01-15", until = "2019-01-30") at test-oai.R:37:5
4. └─oai::list_identifiers(...)
5. └─oai:::while_oai(url, args, token, as, ...)
── Error ('test-oai.R:59:5'): gbif_oai_get_records ─────────────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-clang/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:58:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_get_records("9c4e36c1-d3f9-49ce-8ec1-8c434fa9e6eb") at test-oai.R:59:5
4. └─oai::get_records(...)
5. ├─stats::setNames(...)
6. └─base::lapply(...)
7. └─oai (local) FUN(X[[i]], ...)
8. ├─xml2::read_xml(tt)
9. └─xml2:::read_xml.character(tt)
10. └─xml2:::path_to_connection(x)
11. └─xml2:::check_path(path)
12. └─cli::cli_abort(msg, call = call)
13. └─rlang::abort(...)
── Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms ──
hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)".
1/1 mismatches
x[1]: "Parastrellus hesperus (H.Allen, 1864)"
y[1]: "Pipistrellus hesperus (H.Allen, 1864)"
── Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms ──
hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)".
1/1 mismatches
x[1]: "Parastrellus hesperus (H.Allen, 1864)"
y[1]: "Pipistrellus hesperus (H.Allen, 1864)"
[ FAIL 7 | WARN 2 | SKIP 137 | PASS 1271 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.8.2
Check: tests
Result: ERROR
Running ‘test-all.R’ [42s/101s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("rgbif")
Loading required package: rgbif
[ FAIL 7 | WARN 2 | SKIP 137 | PASS 1271 ]
══ Skipped tests (137) ═════════════════════════════════════════════════════════
• On CRAN (137): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1',
'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:19:3',
'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3',
'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3',
'test-derived_dataset.R:347:3', 'test-downloads.R:3:3',
'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3',
'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3',
'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3',
'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3',
'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5',
'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3',
'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3',
'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5',
'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3',
'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3',
'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3',
'test-name_backbone_checklist.R:273:3',
'test-name_backbone_checklist.R:368:3',
'test-name_backbone_checklist.R:466:3',
'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3',
'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3',
'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3',
'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5',
'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3',
'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3',
'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3',
'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3',
'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3',
'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3',
'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3',
'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3',
'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3',
'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3',
'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3',
'test-occ_download_cancel.R:27:3',
'test-occ_download_dataset_activity.R:4:3',
'test-occ_download_dataset_activity.R:26:3',
'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3',
'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3',
'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3',
'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3',
'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3',
'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3',
'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3',
'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3',
'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3',
'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3',
'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3',
'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3',
'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3',
'test-occ_search.r:101:3', 'test-occ_search.r:114:3',
'test-occ_search.r:128:3', 'test-occ_search.r:143:3',
'test-occ_search.r:161:3', 'test-occ_search.r:178:3',
'test-occ_search.r:195:3', 'test-occ_search.r:214:3',
'test-occ_search.r:231:3', 'test-occ_search.r:248:3',
'test-occ_search.r:266:3', 'test-occ_search.r:283:3',
'test-occ_search.r:300:3', 'test-occ_search.r:318:3',
'test-occ_search.r:336:3', 'test-occ_search.r:354:3',
'test-occ_search.r:369:3', 'test-occ_search.r:386:3',
'test-occ_search.r:436:3', 'test-occ_search.r:510:3',
'test-organizations.r:4:3', 'test-organizations.r:67:3',
'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3',
'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-oai.R:5:5'): gbif_oai_identify ─────────────────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-devel/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:4:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_identify() at test-oai.R:5:5
4. ├─base::as.list(oai::id(url = gboai(), ...))
5. └─oai::id(url = gboai(), ...)
6. ├─plyr::rbind.fill(lapply(url, id_, as = as, ...))
7. └─base::lapply(url, id_, as = as, ...)
8. └─oai (local) FUN(X[[i]], ...)
9. ├─oai:::get_headers(xml_children(xml2::read_xml(tt))[[3]])
10. │ ├─base::lapply(...)
11. │ └─xml2::xml_children(m)
12. │ └─xml2:::nodeset_apply(x, function(x) .Call(node_children, x, TRUE))
13. ├─xml2::xml_children(xml2::read_xml(tt))
14. │ └─xml2:::nodeset_apply(x, function(x) .Call(node_children, x, TRUE))
15. ├─xml2::read_xml(tt)
16. └─xml2:::read_xml.character(tt)
17. └─xml2:::path_to_connection(x)
18. └─xml2:::check_path(path)
19. └─cli::cli_abort(msg, call = call)
20. └─rlang::abort(...)
── Error ('test-oai.R:15:5'): gbif_oai_list_metadataformats ────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-devel/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:14:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_metadataformats() at test-oai.R:15:5
4. └─oai::list_metadataformats(url = gboai(), id = id, ...)
5. └─oai:::one_mf(id, url, ...)
6. ├─xml2::read_xml(out)
7. └─xml2:::read_xml.character(out)
8. └─xml2:::path_to_connection(x)
9. └─xml2:::check_path(path)
10. └─cli::cli_abort(msg, call = call)
11. └─rlang::abort(...)
── Error ('test-oai.R:25:5'): gbif_oai_list_sets ───────────────────────────────
Error in `while_oai(url, args, token, as, ...)`: cannot parse downloaded XML, dumped raw XML to file ./oaidump_2025-07-21_07-11-15.48876913ebd271a4e3bexml
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:24:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_sets() at test-oai.R:25:5
4. └─oai::list_sets(url = gboai(), token = token, as = as, ...)
5. └─oai:::while_oai(url, args, token, as, ...)
── Error ('test-oai.R:37:5'): gbif_oai_list_identifiers ────────────────────────
Error in `while_oai(url, args, token, as, ...)`: cannot parse downloaded XML, dumped raw XML to file ./oaidump_2025-07-21_07-11-15.86318613ebd271d1ed9exml
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:35:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_list_identifiers(from = "2019-01-15", until = "2019-01-30") at test-oai.R:37:5
4. └─oai::list_identifiers(...)
5. └─oai:::while_oai(url, args, token, as, ...)
── Error ('test-oai.R:59:5'): gbif_oai_get_records ─────────────────────────────
Error in `path_to_connection(x)`: '' does not exist in current working directory
('/data/gannet/ripley/R/packages/tests-devel/rgbif.Rcheck/tests/testthat').
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-oai.R:58:3
2. │ └─cassette$call_block(...)
3. └─rgbif::gbif_oai_get_records("9c4e36c1-d3f9-49ce-8ec1-8c434fa9e6eb") at test-oai.R:59:5
4. └─oai::get_records(...)
5. ├─stats::setNames(...)
6. └─base::lapply(...)
7. └─oai (local) FUN(X[[i]], ...)
8. ├─xml2::read_xml(tt)
9. └─xml2:::read_xml.character(tt)
10. └─xml2:::path_to_connection(x)
11. └─xml2:::check_path(path)
12. └─cli::cli_abort(msg, call = call)
13. └─rlang::abort(...)
── Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms ──
hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)".
1/1 mismatches
x[1]: "Parastrellus hesperus (H.Allen, 1864)"
y[1]: "Pipistrellus hesperus (H.Allen, 1864)"
── Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms ──
hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)".
1/1 mismatches
x[1]: "Parastrellus hesperus (H.Allen, 1864)"
y[1]: "Pipistrellus hesperus (H.Allen, 1864)"
[ FAIL 7 | WARN 2 | SKIP 137 | PASS 1271 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc