Last updated on 2024-07-19 13:50:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 15.09 | 149.37 | 164.46 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 11.08 | 111.50 | 122.58 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 202.90 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 202.69 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 15.00 | 129.00 | 144.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 16.67 | 144.63 | 161.30 | ERROR | |
| r-release-linux-x86_64 | 2.0.2 | 9.89 | 141.20 | 151.09 | OK | |
| r-release-macos-arm64 | 2.0.2 | 69.00 | OK | |||
| r-release-macos-x86_64 | 2.0.2 | 110.00 | OK | |||
| r-release-windows-x86_64 | 2.0.2 | 13.00 | 129.00 | 142.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 79.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.0.2 | 161.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.0.2 | 18.00 | 160.00 | 178.00 | OK |
Version: 2.0.2
Check: examples
Result: ERROR
Running examples in ‘galah-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print_galah_objects
> ### Title: Print galah objects
> ### Aliases: print_galah_objects print.data_request print.files_request
> ### print.metadata_request print.query print.computed_query
> ### print.query_set print.galah_config
>
> ### ** Examples
>
> # The most common way to start a pipe is with `galah_call()`
> # later functions update the `data_request` object
> galah_call() |> # same as calling `request_data()`
+ filter(year >= 2020) |>
+ group_by(year) |>
+ count()
Object of type `data_request` containing:
• type occurrences-count
• filter year >= 2020
• group_by year>
> # Metadata requests are formatted in a similar way
> request_metadata() |>
+ filter(field == basisOfRecord) |>
+ unnest()
Object of type `metadata_request` containing:
• type fields-unnest
• filter field == basisOfRecord>
> # Queries are converted into a `query_set` by `collapse()`
> x <- galah_call() |> # same as calling `request_data()`
+ filter(year >= 2020) |>
+ count() |>
+ collapse()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [biocache-ws.ala.org.au] Operation timed out after 20000 milliseconds with 0 bytes received
Backtrace:
▆
1. ├─dplyr::collapse(count(filter(galah_call(), year >= 2020)))
2. └─galah:::collapse.data_request(...)
3. ├─galah:::parse_query(parse_checks(build_checks(query_set)))
4. ├─galah:::parse_checks(build_checks(query_set))
5. │ └─base::grepl("^data/", .query$type)
6. │ └─base::is.factor(x)
7. └─galah:::build_checks(query_set)
8. └─galah:::parse_metadata(names_vec, .query)
9. └─base::lapply(.query[which(metadata_lookup)], collect)
10. ├─dplyr (local) FUN(X[[i]], ...)
11. └─galah:::collect.query(X[[i]], ...)
12. ├─dplyr::collect(compute(x), wait = wait, file = file)
13. └─galah:::collect.computed_query(compute(x), wait = wait, file = file)
14. └─galah:::collect_fields(x)
15. ├─dplyr::bind_rows(query_API(.query))
16. │ └─rlang::list2(...)
17. └─galah:::query_API(.query)
18. └─galah:::query_API_internal(.query)
19. └─httr2::req_perform(req_timeout(query, seconds = 20), verbosity = 0)
20. └─base::tryCatch(...)
21. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
22. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. └─value[[3L]](cond)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(galah)
galah: version 2.0.2
ℹ Default node set to ALA (ala.org.au).
ℹ See all supported GBIF nodes with `show_all(atlases)`.
ℹ To change nodes, use e.g. `galah_config(atlas = "GBIF")`.
Attaching package: 'galah'
The following object is masked from 'package:stats':
filter
> library(dplyr)
Attaching package: 'dplyr'
The following object is masked from 'package:galah':
desc
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> galah_config(directory = tempdir(),
+ email = "ala4r@ala.org.au",
+ caching = FALSE,
+ atlas = "Australia",
+ verbose = FALSE,
+ run_checks = TRUE)
> test_check("galah")
[ FAIL 1 | WARN 0 | SKIP 319 | PASS 231 ]
══ Skipped tests (319) ═════════════════════════════════════════════════════════
• On CRAN (319): 'test-atlas_counts.R:4:3', 'test-atlas_counts.R:14:3',
'test-atlas_counts.R:21:3', 'test-atlas_counts.R:30:3',
'test-atlas_counts.R:43:3', 'test-atlas_counts.R:55:3',
'test-atlas_counts.R:68:3', 'test-atlas_counts.R:82:3',
'test-atlas_counts.R:96:3', 'test-atlas_counts.R:110:3',
'test-atlas_counts.R:128:3', 'test-atlas_counts.R:154:3',
'test-atlas_counts.R:168:3', 'test-atlas_counts.R:195:3',
'test-atlas_media.R:6:3', 'test-atlas_media.R:18:3',
'test-atlas_media.R:34:3', 'test-atlas_media.R:119:3',
'test-atlas_media.R:130:3', 'test-atlas_media.R:151:3',
'test-atlas_occurrences.R:36:3', 'test-atlas_occurrences.R:63:3',
'test-atlas_occurrences.R:96:3', 'test-atlas_occurrences.R:116:3',
'test-atlas_occurrences.R:162:3', 'test-atlas_occurrences.R:181:3',
'test-atlas_occurrences.R:214:3', 'test-atlas_species.R:2:3',
'test-atlas_species.R:9:3', 'test-atlas_species.R:16:3',
'test-atlas_species.R:35:3', 'test-atlas_species.R:56:3',
'test-atlas_species.R:67:3', 'test-atlas_species.R:89:3',
'test-atlas_taxonomy.R:27:3', 'test-atlas_taxonomy.R:38:3',
'test-count_arrange_slice.R:2:3', 'test-count_arrange_slice.R:15:3',
'test-count_arrange_slice.R:29:3', 'test-count_arrange_slice.R:43:3',
'test-count_arrange_slice.R:57:3', 'test-count_arrange_slice.R:71:3',
'test-count_arrange_slice.R:101:3', 'test-count_arrange_slice.R:133:3',
'test-galah_apply_profile.R:2:3', 'test-galah_apply_profile.R:21:3',
'test-galah_apply_profile.R:40:3', 'test-galah_apply_profile.R:58:3',
'test-galah_apply_profile.R:66:3', 'test-galah_apply_profile.R:77:3',
'test-galah_call.R:21:3', 'test-galah_call.R:34:3', 'test-galah_call.R:47:3',
'test-galah_config.R:19:3', 'test-galah_config.R:30:3',
'test-galah_filter.R:12:3', 'test-galah_filter.R:33:3',
'test-galah_filter.R:79:3', 'test-galah_filter.R:223:3',
'test-galah_filter.R:238:3', 'test-galah_filter.R:247:3',
'test-galah_filter.R:305:3', 'test-galah_filter.R:334:3',
'test-galah_filter.R:348:3', 'test-galah_filter.R:364:3',
'test-galah_group_by.R:9:3', 'test-galah_group_by.R:22:3',
'test-galah_group_by.R:33:3', 'test-galah_group_by.R:46:3',
'test-galah_group_by.R:55:3', 'test-galah_group_by.R:67:3',
'test-galah_group_by.R:83:3', 'test-galah_group_by.R:96:3',
'test-galah_identify.R:43:3', 'test-galah_identify.R:55:3',
'test-galah_identify.R:74:3', 'test-galah_identify.R:90:3',
'test-galah_identify.R:106:3', 'test-galah_polygon.R:19:3',
'test-galah_select.R:7:3', 'test-galah_select.R:23:3',
'test-galah_select.R:35:3', 'test-galah_select.R:47:3',
'test-galah_select.R:58:3', 'test-galah_select.R:70:3',
'test-galah_select.R:82:3', 'test-galah_select.R:92:3',
'test-galah_select.R:112:3', 'test-galah_select.R:123:3',
'test-galah_select.R:134:3', 'test-galah_select.R:147:3',
'test-galah_select.R:160:3', 'test-galah_select.R:171:3',
'test-galah_select.R:182:3', 'test-galah_select.R:194:3',
'test-galah_select.R:202:3', 'test-galah_select.R:212:3',
'test-galah_select.R:222:3', 'test-international-Austria.R:9:3',
'test-international-Austria.R:20:3', 'test-international-Austria.R:31:3',
'test-international-Austria.R:42:3', 'test-international-Austria.R:53:3',
'test-international-Austria.R:65:3', 'test-international-Austria.R:76:3',
'test-international-Austria.R:87:3', 'test-international-Austria.R:102:3',
'test-international-Austria.R:111:3', 'test-international-Austria.R:120:3',
'test-international-Austria.R:130:3', 'test-international-Austria.R:140:3',
'test-international-Austria.R:149:3', 'test-international-Austria.R:159:3',
'test-international-Austria.R:175:3', 'test-international-Austria.R:187:3',
'test-international-Austria.R:206:3', 'test-international-Austria.R:226:3',
'test-international-Austria.R:256:3', 'test-international-Brazil.R:9:3',
'test-international-Brazil.R:18:3', 'test-international-Brazil.R:27:3',
'test-international-Brazil.R:36:3', 'test-international-Brazil.R:49:3',
'test-international-Brazil.R:62:3', 'test-international-Brazil.R:71:3',
'test-international-Brazil.R:80:3', 'test-international-Brazil.R:89:3',
'test-international-Brazil.R:106:3', 'test-international-Brazil.R:115:3',
'test-international-Brazil.R:124:3', 'test-international-Brazil.R:148:3',
'test-international-Brazil.R:160:3', 'test-international-Brazil.R:178:3',
'test-international-Estonia.R:9:3', 'test-international-Estonia.R:18:3',
'test-international-Estonia.R:27:3', 'test-international-Estonia.R:36:3',
'test-international-Estonia.R:49:3', 'test-international-Estonia.R:66:3',
'test-international-Estonia.R:75:3', 'test-international-Estonia.R:84:3',
'test-international-Estonia.R:93:3', 'test-international-Estonia.R:102:3',
'test-international-Estonia.R:111:3', 'test-international-Estonia.R:123:3',
'test-international-France.R:9:3', 'test-international-France.R:18:3',
'test-international-France.R:27:3', 'test-international-France.R:36:3',
'test-international-France.R:49:3', 'test-international-France.R:66:3',
'test-international-France.R:75:3', 'test-international-France.R:84:3',
'test-international-France.R:93:3', 'test-international-France.R:102:3',
'test-international-France.R:111:3', 'test-international-France.R:130:3',
'test-international-France.R:143:3', 'test-international-France.R:157:3',
'test-international-GBIF.R:23:3', 'test-international-GBIF.R:39:3',
'test-international-GBIF.R:50:3', 'test-international-GBIF.R:79:3',
'test-international-GBIF.R:90:3', 'test-international-GBIF.R:97:3',
'test-international-GBIF.R:104:3', 'test-international-GBIF.R:113:3',
'test-international-GBIF.R:120:3', 'test-international-GBIF.R:128:3',
'test-international-GBIF.R:139:3', 'test-international-GBIF.R:161:3',
'test-international-GBIF.R:183:3', 'test-international-GBIF.R:220:3',
'test-international-GBIF.R:249:3', 'test-international-GBIF.R:273:3',
'test-international-GBIF.R:288:3', 'test-international-GBIF.R:310:3',
'test-international-GBIF.R:334:3', 'test-international-GBIF.R:342:3',
'test-international-Guatemala.R:9:3', 'test-international-Guatemala.R:21:3',
'test-international-Guatemala.R:30:3', 'test-international-Guatemala.R:39:3',
'test-international-Guatemala.R:48:3', 'test-international-Guatemala.R:57:3',
'test-international-Guatemala.R:74:3', 'test-international-Guatemala.R:83:3',
'test-international-Guatemala.R:92:3',
'test-international-Guatemala.R:102:3',
'test-international-Guatemala.R:111:3',
'test-international-Guatemala.R:137:3',
'test-international-Guatemala.R:150:3',
'test-international-Guatemala.R:161:3', 'test-international-Portugal.R:9:3',
'test-international-Portugal.R:18:3', 'test-international-Portugal.R:27:3',
'test-international-Portugal.R:37:3', 'test-international-Portugal.R:46:3',
'test-international-Portugal.R:55:3', 'test-international-Portugal.R:72:3',
'test-international-Portugal.R:81:3', 'test-international-Portugal.R:90:3',
'test-international-Portugal.R:100:3', 'test-international-Portugal.R:109:3',
'test-international-Portugal.R:118:3', 'test-international-Portugal.R:138:3',
'test-international-Spain.R:9:3', 'test-international-Spain.R:21:3',
'test-international-Spain.R:30:3', 'test-international-Spain.R:39:3',
'test-international-Spain.R:48:3', 'test-international-Spain.R:57:3',
'test-international-Spain.R:66:3', 'test-international-Spain.R:75:3',
'test-international-Spain.R:84:3', 'test-international-Spain.R:93:3',
'test-international-Spain.R:102:3', 'test-international-Spain.R:111:3',
'test-international-Spain.R:122:3', 'test-international-Spain.R:131:3',
'test-international-Spain.R:141:3', 'test-international-Spain.R:151:3',
'test-international-Spain.R:160:3', 'test-international-Spain.R:169:3',
'test-international-Spain.R:189:3', 'test-international-Spain.R:217:3',
'test-international-Spain.R:233:3', 'test-international-Spain.R:249:3',
'test-international-Sweden.R:9:3', 'test-international-Sweden.R:18:3',
'test-international-Sweden.R:27:3', 'test-international-Sweden.R:36:3',
'test-international-Sweden.R:46:3', 'test-international-Sweden.R:55:3',
'test-international-Sweden.R:64:3', 'test-international-Sweden.R:73:3',
'test-international-Sweden.R:86:3', 'test-international-Sweden.R:95:3',
'test-international-Sweden.R:104:3', 'test-international-Sweden.R:116:3',
'test-international-Sweden.R:127:3', 'test-international-Sweden.R:137:3',
'test-international-Sweden.R:146:3', 'test-international-Sweden.R:156:3',
'test-international-Sweden.R:165:3', 'test-international-Sweden.R:174:3',
'test-international-Sweden.R:192:3', 'test-international-Sweden.R:204:3',
'test-international-Sweden.R:220:3', 'test-international-Sweden.R:239:3',
'test-international-UK.R:9:3', 'test-international-UK.R:21:3',
'test-international-UK.R:30:3', 'test-international-UK.R:39:3',
'test-international-UK.R:48:3', 'test-international-UK.R:57:3',
'test-international-UK.R:70:3', 'test-international-UK.R:79:3',
'test-international-UK.R:88:3', 'test-international-UK.R:97:3',
'test-international-UK.R:105:3', 'test-international-UK.R:110:3',
'test-international-UK.R:119:3', 'test-international-UK.R:128:3',
'test-international-UK.R:137:3', 'test-international-UK.R:146:3',
'test-international-UK.R:168:3', 'test-international-UK.R:180:3',
'test-international-UK.R:193:3', 'test-masked-functions.R:2:3',
'test-masked-functions.R:34:3', 'test-masked-functions.R:41:3',
'test-request_metadata_unnest.R:2:3', 'test-request_metadata_unnest.R:30:3',
'test-request_metadata_unnest.R:47:3', 'test-request_metadata_unnest.R:62:3',
'test-request_metadata_unnest.R:80:3', 'test-search_all.R:6:3',
'test-search_all.R:11:3', 'test-search_all.R:31:3', 'test-search_all.R:37:3',
'test-search_all.R:53:3', 'test-search_all.R:68:3', 'test-search_all.R:83:3',
'test-search_all.R:98:3', 'test-search_all.R:113:3',
'test-search_all.R:128:3', 'test-search_all.R:133:3',
'test-search_all.R:148:3', 'test-search_all.R:163:3',
'test-search_all.R:178:3', 'test-search_all.R:193:3',
'test-search_all.R:208:3', 'test-search_taxa.R:6:3',
'test-search_taxa.R:12:3', 'test-search_taxa.R:18:3',
'test-search_taxa.R:25:3', 'test-search_taxa.R:33:3',
'test-search_taxa.R:40:3', 'test-search_taxa.R:48:3',
'test-search_taxa.R:60:3', 'test-search_taxa.R:70:3',
'test-search_taxa.R:82:3', 'test-search_taxa.R:89:3',
'test-search_taxa.R:94:3', 'test-search_taxa.R:103:3',
'test-show_all.R:11:3', 'test-show_all.R:18:3', 'test-show_values.R:2:3',
'test-show_values.R:11:3', 'test-show_values.R:24:3',
'test-show_values.R:37:3', 'test-show_values.R:50:3',
'test-show_values.R:56:3', 'test-show_values.R:70:3',
'test-show_values.R:84:3', 'test-show_values.R:98:3',
'test-show_values.R:106:3', 'test-show_values.R:119:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-atlas_occurrences.R:27:3'): collapse(type = 'occurrences') creates an object, but doesn't ping an API ──
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(req_timeout(query, seconds = 20), verbosity = 0)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [api.ala.org.au] Operation timed out after 20002 milliseconds with 0 bytes received
Backtrace:
▆
1. ├─dplyr::collapse(identify(galah_call(), "Perameles")) at test-atlas_occurrences.R:27:3
2. └─galah:::collapse.data_request(identify(galah_call(), "Perameles"))
3. ├─galah:::parse_query(parse_checks(build_checks(query_set)))
4. ├─galah:::parse_checks(build_checks(query_set))
5. │ └─base::grepl("^data/", .query$type)
6. │ └─base::is.factor(x)
7. └─galah:::build_checks(query_set)
8. └─galah:::parse_metadata(names_vec, .query)
9. └─base::lapply(.query[which(metadata_lookup)], collect)
10. ├─dplyr (local) FUN(X[[i]], ...)
11. └─galah:::collect.query(X[[i]], ...)
12. ├─dplyr::collect(compute(x), wait = wait, file = file)
13. └─galah:::collect.computed_query(compute(x), wait = wait, file = file)
14. └─galah:::collect_reasons(x)
15. ├─dplyr::bind_rows(query_API(.query))
16. │ └─rlang::list2(...)
17. └─galah:::query_API(.query)
18. └─galah:::query_API_internal(.query)
19. └─httr2::req_perform(req_timeout(query, seconds = 20), verbosity = 0)
20. └─base::tryCatch(...)
21. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
22. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. └─value[[3L]](cond)
[ FAIL 1 | WARN 0 | SKIP 319 | PASS 231 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64