Last updated on 2025-02-01 12:48:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.2 | 14.48 | 140.93 | 155.41 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.2 | 9.94 | 95.05 | 104.99 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.2 | 279.39 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.2 | 271.94 | OK | |||
| r-devel-windows-x86_64 | 1.3.2 | 20.00 | 323.00 | 343.00 | OK | |
| r-patched-linux-x86_64 | 1.3.2 | 14.95 | 144.59 | 159.54 | NOTE | |
| r-release-linux-x86_64 | 1.3.2 | 14.16 | 144.16 | 158.32 | NOTE | |
| r-release-macos-arm64 | 1.3.2 | 286.00 | OK | |||
| r-release-macos-x86_64 | 1.3.2 | 430.00 | OK | |||
| r-release-windows-x86_64 | 1.3.2 | 17.00 | 311.00 | 328.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.2 | 304.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.3.2 | 435.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.3.2 | 21.00 | 346.00 | 367.00 | OK |
Version: 1.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ecocomDP)
>
> test_check("ecocomDP")
[ FAIL 95 | WARN 3 | SKIP 11 | PASS 459 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test_convert_to_dwca.R:8:3', 'test_create_eml.R:8:3',
'test_read_data.R:6:3', 'test_search_data.R:8:3', 'test_search_data.R:22:3',
'test_search_data.R:37:3', 'test_search_data.R:49:3',
'test_search_data.R:73:3', 'test_validate_arguments.R:322:3',
'test_validate_arguments.R:424:3', 'test_validate_data.R:421:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_flatten_data.R:108:5'): Non-required columns ───────────────────
Error in `dplyr::left_join(., tables$location %>% dplyr::select_if(not_all_NAs),
by = "location_id", suffix = c("", "_location"))`: Join columns in `x` must be present in the data.
✖ Problem with `location_id`.
Backtrace:
▆
1. ├─ecocomDP::flatten_data(tbls) at test_flatten_data.R:108:5
2. │ └─ecocomDP:::flatten_tables(data)
3. │ └─all_merged %>% ...
4. ├─dplyr::left_join(...)
5. └─dplyr:::left_join.data.frame(...)
6. └─dplyr:::join_mutate(...)
7. └─dplyr:::join_cols(...)
8. └─dplyr:::check_join_vars(by$x, x_names, by$condition, "x", error_call = error_call)
9. └─rlang::abort(bullets, call = error_call)
── Error ('test_read_data.R:73:3'): Reads from 1 local .rds ────────────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. └─ecocomDP::read_data(from = rdspath) at test_read_data.R:73:3
2. └─ecocomDP::validate_data(dataset = d)
3. └─ecocomDP:::validate_primary_keys(d)
4. └─base::lapply(...)
5. └─ecocomDP (local) FUN(X[[i]], ...)
6. ├─data.list[[x]][[primary_key]]
7. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
8. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
9. └─tibble:::vectbl_as_col_location2(...)
10. ├─tibble:::subclass_col_index_errors(...)
11. │ └─base::withCallingHandlers(...)
12. └─vctrs::vec_as_location2(j, n, names, call = call)
13. └─vctrs:::result_get(...)
14. └─rlang::cnd_signal(x$err)
── Error ('test_read_data.R:106:3'): Reads from > 1 local .rds ─────────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. └─ecocomDP::read_data(from = rdspath) at test_read_data.R:106:3
2. └─ecocomDP::validate_data(dataset = d[[i]])
3. └─ecocomDP:::validate_primary_keys(d)
4. └─base::lapply(...)
5. └─ecocomDP (local) FUN(X[[i]], ...)
6. ├─data.list[[x]][[primary_key]]
7. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
8. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
9. └─tibble:::vectbl_as_col_location2(...)
10. ├─tibble:::subclass_col_index_errors(...)
11. │ └─base::withCallingHandlers(...)
12. └─vctrs::vec_as_location2(j, n, names, call = call)
13. └─vctrs:::result_get(...)
14. └─rlang::cnd_signal(x$err)
── Error ('test_read_data.R:142:3'): Reads from 1 local .csv directories ───────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = tempdir()) at test_read_data.R:142:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:168:3'): Reads from > 1 local .csv directories ─────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = tempdir()) at test_read_data.R:168:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:198:3'): Reads tables with valid names in path ─────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = readpath) at test_read_data.R:198:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:221:3'): Ignores tables with invalid names in path ──
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. ├─testthat::expect_warning(read_data(from = readpath), regexp = "Validation issues") at test_read_data.R:221:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ecocomDP::read_data(from = readpath)
7. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
8. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
9. ├─base::as.Date(x, ...)
10. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:236:3'): Has datetime parsing option ───────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_read_data.R:236:3
2. │ └─base::withCallingHandlers(...)
3. └─ecocomDP::read_data(from = paste0(tempdir(), "/d.rds"), parse_datetime = TRUE)
4. └─ecocomDP::validate_data(dataset = d[[i]])
5. └─ecocomDP:::validate_primary_keys(d)
6. └─base::lapply(...)
7. └─ecocomDP (local) FUN(X[[i]], ...)
8. ├─data.list[[x]][[primary_key]]
9. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
10. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
11. └─tibble:::vectbl_as_col_location2(...)
12. ├─tibble:::subclass_col_index_errors(...)
13. │ └─base::withCallingHandlers(...)
14. └─vctrs::vec_as_location2(j, n, names, call = call)
15. └─vctrs:::result_get(...)
16. └─rlang::cnd_signal(x$err)
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Error ('test_validate_data.R:92:9'): validate_column_presence() ─────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in ``[[<-`(`*tmp*`, column, value = NULL)`: Can't assign column with `column`.
✖ Subscript `column` must be a location, not a character `NA`.
Backtrace:
▆
1. ├─base::`[[<-`(`*tmp*`, column, value = `<NULL>`) at test_validate_data.R:92:9
2. └─tibble:::`[[<-.tbl_df`(`*tmp*`, column, value = `<NULL>`) at test_validate_data.R:92:9
3. └─tibble:::vectbl_as_col_location2(...)
4. ├─tibble:::subclass_col_index_errors(...)
5. │ └─base::withCallingHandlers(...)
6. └─vctrs::vec_as_location2(j, n, names, call = call)
7. └─vctrs:::result_get(...)
8. └─rlang::cnd_signal(x$err)
── Error ('test_validate_data.R:187:5'): validate_primary_keys() ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_null(validate_primary_keys(d)) at test_validate_data.R:187:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ecocomDP:::validate_primary_keys(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─data.list[[x]][[primary_key]]
8. └─base::`[[.data.frame`(data.list[[x]], primary_key)
9. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Failure ('test_validate_data.R:221:5'): validate_composite_keys() ───────────
validate_composite_keys(d) is not NULL
`actual` is a character vector ('Composite keys. The composite keys composed of the columns variable_name, in the table location_ancillary contain non-unique values in rows: 2 3 4 5 6 7 8')
`expected` is NULL
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`: TRUE TRUE
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Error ('test_validate_data.R:259:5'): validate_referential_integrity() ──────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_null(validate_referential_integrity(d)) at test_validate_data.R:259:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ecocomDP:::validate_referential_integrity(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─stats::na.omit(data.list[[x]][[primary_key]])
8. ├─data.list[[x]][[primary_key]]
9. └─base::`[[.data.frame`(data.list[[x]], primary_key)
10. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_validate_data.R:489:5'): validate_data ─────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(validate_data(dataset = d)) at test_validate_data.R:489:5
2. │ └─base::withCallingHandlers(...)
3. └─ecocomDP::validate_data(dataset = d)
4. └─ecocomDP:::validate_primary_keys(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─data.list[[x]][[primary_key]]
8. └─base::`[[.data.frame`(data.list[[x]], primary_key)
9. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
[ FAIL 95 | WARN 3 | SKIP 11 | PASS 459 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ecocomDP)
>
> test_check("ecocomDP")
[ FAIL 134 | WARN 3 | SKIP 11 | PASS 467 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test_convert_to_dwca.R:8:3', 'test_create_eml.R:8:3',
'test_read_data.R:6:3', 'test_search_data.R:8:3', 'test_search_data.R:22:3',
'test_search_data.R:37:3', 'test_search_data.R:49:3',
'test_search_data.R:73:3', 'test_validate_arguments.R:322:3',
'test_validate_arguments.R:424:3', 'test_validate_data.R:421:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_flatten_data.R:108:5'): Non-required columns ───────────────────
Error in `dplyr::left_join(., tables$location %>% dplyr::select_if(not_all_NAs),
by = "location_id", suffix = c("", "_location"))`: Join columns in `x` must be present in the data.
✖ Problem with `location_id`.
Backtrace:
▆
1. ├─ecocomDP::flatten_data(tbls) at test_flatten_data.R:108:5
2. │ └─ecocomDP:::flatten_tables(data)
3. │ └─all_merged %>% ...
4. ├─dplyr::left_join(...)
5. └─dplyr:::left_join.data.frame(...)
6. └─dplyr:::join_mutate(...)
7. └─dplyr:::join_cols(...)
8. └─dplyr:::check_join_vars(by$x, x_names, by$condition, "x", error_call = error_call)
9. └─rlang::abort(bullets, call = error_call)
── Error ('test_read_data.R:73:3'): Reads from 1 local .rds ────────────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. └─ecocomDP::read_data(from = rdspath) at test_read_data.R:73:3
2. └─ecocomDP::validate_data(dataset = d)
3. └─ecocomDP:::validate_primary_keys(d)
4. └─base::lapply(...)
5. └─ecocomDP (local) FUN(X[[i]], ...)
6. ├─data.list[[x]][[primary_key]]
7. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
8. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
9. └─tibble:::vectbl_as_col_location2(...)
10. ├─tibble:::subclass_col_index_errors(...)
11. │ └─base::withCallingHandlers(...)
12. └─vctrs::vec_as_location2(j, n, names, call = call)
13. └─vctrs:::result_get(...)
14. └─rlang::cnd_signal(x$err)
── Error ('test_read_data.R:106:3'): Reads from > 1 local .rds ─────────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. └─ecocomDP::read_data(from = rdspath) at test_read_data.R:106:3
2. └─ecocomDP::validate_data(dataset = d[[i]])
3. └─ecocomDP:::validate_primary_keys(d)
4. └─base::lapply(...)
5. └─ecocomDP (local) FUN(X[[i]], ...)
6. ├─data.list[[x]][[primary_key]]
7. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
8. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
9. └─tibble:::vectbl_as_col_location2(...)
10. ├─tibble:::subclass_col_index_errors(...)
11. │ └─base::withCallingHandlers(...)
12. └─vctrs::vec_as_location2(j, n, names, call = call)
13. └─vctrs:::result_get(...)
14. └─rlang::cnd_signal(x$err)
── Error ('test_read_data.R:142:3'): Reads from 1 local .csv directories ───────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = tempdir()) at test_read_data.R:142:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:168:3'): Reads from > 1 local .csv directories ─────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = tempdir()) at test_read_data.R:168:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:198:3'): Reads tables with valid names in path ─────
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. └─ecocomDP::read_data(from = readpath) at test_read_data.R:198:3
2. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
3. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
4. ├─base::as.Date(x, ...)
5. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:221:3'): Ignores tables with invalid names in path ──
Error in `as.Date.default(x, ...)`: do not know how to convert 'x' to class "Date"
Backtrace:
▆
1. ├─testthat::expect_warning(read_data(from = readpath), regexp = "Validation issues") at test_read_data.R:221:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ecocomDP::read_data(from = readpath)
7. ├─lubridate::as_date(d[[x]]$tables[[y]][[z]])
8. └─lubridate::as_date(d[[x]]$tables[[y]][[z]])
9. ├─base::as.Date(x, ...)
10. └─base::as.Date.default(x, ...)
── Error ('test_read_data.R:236:3'): Has datetime parsing option ───────────────
<vctrs_error_subscript_type/vctrs_error_subscript/rlang_error/error/condition>
Error in `data.list[[x]][[primary_key]]`: Can't extract column with `primary_key`.
✖ Subscript `primary_key` must be size 1, not 2.
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_read_data.R:236:3
2. │ └─base::withCallingHandlers(...)
3. └─ecocomDP::read_data(from = paste0(tempdir(), "/d.rds"), parse_datetime = TRUE)
4. └─ecocomDP::validate_data(dataset = d[[i]])
5. └─ecocomDP:::validate_primary_keys(d)
6. └─base::lapply(...)
7. └─ecocomDP (local) FUN(X[[i]], ...)
8. ├─data.list[[x]][[primary_key]]
9. └─tibble:::`[[.tbl_df`(data.list[[x]], primary_key)
10. └─tibble:::tbl_subset2(x, j = i, j_arg = substitute(i))
11. └─tibble:::vectbl_as_col_location2(...)
12. ├─tibble:::subclass_col_index_errors(...)
13. │ └─base::withCallingHandlers(...)
14. └─vctrs::vec_as_location2(j, n, names, call = call)
15. └─vctrs:::result_get(...)
16. └─rlang::cnd_signal(x$err)
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:36:7'): validate_table_presence() ────────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:93:9'): validate_column_presence() ───────────
stringr::str_detect(...) is not TRUE
`actual`:
`expected`: TRUE
── Error ('test_validate_data.R:187:5'): validate_primary_keys() ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_null(validate_primary_keys(d)) at test_validate_data.R:187:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ecocomDP:::validate_primary_keys(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─data.list[[x]][[primary_key]]
8. └─base::`[[.data.frame`(data.list[[x]], primary_key)
9. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Failure ('test_validate_data.R:221:5'): validate_composite_keys() ───────────
validate_composite_keys(d) is not NULL
`actual` is a character vector ('Composite keys. The composite keys composed of the columns observation_id, in the table observation_ancillary contain non-unique values in rows: 2 3 5 6 8 9 11 12 14 15 17 18 20 21 23 24 26 27 29 30 32 33 35 36 38 39 41 42 44 45 47 48 50 51 53 54 56 57 59 60 62 63 65 66 68 69 71 72 74 75 77 78 80 81 83 84 86 87 89 90 92 93 95 96 98 99 101 102 104 105 107 108 110 111 113 114 116 117 119 120 122 123 125 126 128 129 131 132 134 135 137 138 140 141 143 144 146 147 149 150 152 153 155 156 158 159 161 162 164 165 167 168 170 171 173 174 176 177 179 180 182 183 185 186 188 189 191 192 194 195 197 198 200 201 203 204 206 207 209 210 212 213 215 216 218 219 221 222 224 225 227 228 230 231 233 234 236 237 239 240 242 243 245 246 248 249 251 252 254 255 257 258 260 261 263 264 266 267 269 270 272 273 275 276 278 279 281 282 284 285 287 288 290 291 293 294 296 297 299 300 302 303 305 306 308 309 311 312 314 315 317 318 320 321 323 324 326 327 329 330 332 333 335 336 338 339 341 342 344 345 347 348 350 351 353 354 356 357 359 360 362 363 365 366 368 369 371 372 374 375 377 378 380 381 383 384 386 387 389 390 392 393 395 396 398 399 401 402 404 405 407 408 410 411 413 414 416 417 419 420 422 423 425 426 428 429 431 432 434 435 437 438 440 441 443 444 446 447 449 450 452 453 455 456 458 459 461 462 464 465 467 468 470 471 473 474 476 477 479 480 482 483 485 486 488 489 491 492 494 495 497 498 500 501 503 504 506 507 509 510 512 513 515 516 518 519 521 522 524 525 527 528 530 531 533 534 536 537 539 540 542 543 545 546 548 549 551 552 554 555 557 558 560 561 563 564 566 567 569 570 572 573 575 576 578 579 581 582 584 585 587 588 590 591 593 594 596 597 599 600 602 603 605 606 608 609 611 612 614 615 617 618 620 621 623 624 626 627 629 630 632 633 635 636 638 639 641 642 644 645 647 648 650 651 653 654 656 657 659 660 662 663 665 666 668 669 671 672 674 675 677 678 680 681 683 684 686 687 689 690 692 693 695 696 698 699 701 702 704 705 707 708 710 711 713 714 716 717 719 720 722 723 725 726 728 729 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8585 8586 8588 8589 8591 8592 8594 8595 8597 8598 8600 8601 8603 8604 8606 8607 8609 8610 8612 8613 8615 8616 8618 8619 8621 8622 8624 8625 8627 8628 8630 8631 8633 8634 8636 8637 8639 8640 8642 8643 8645 8646 8648 8649 8651 8652 8654 8655 8657 8658 8660 8661 8663 8664 8666 8667 8669 8670 8672 8673 8675 8676 8678 8679 8681 8682 8684 8685 8687 8688 8690 8691 8693 8694 8696 8697 8699 8700 8702 8703 8705 8706 8708 8709 8711 8712 8714 8715 8717 8718 8720 8721 8723 8724 8726 8727 8729 8730 8732 8733 8735 8736 8738 8739 8741 8742 8744 8745 8747 8748 8750 8751 8753 8754 8756 8757 8759 8760 8762 8763 8765 8766 8768 8769 8771 8772 8774 8775 8777 8778 8780 8781 8783 8784 8786 8787 8789 8790 8792 8793')
`expected` is NULL
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`: TRUE TRUE
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test_validate_data.R:237:9'): validate_composite_keys() ───────────
stringr::str_detect(validate_composite_keys(d), "Composite keys. The composite keys composed of the columns .+") is not TRUE
`actual`:
`expected`: TRUE
── Error ('test_validate_data.R:259:5'): validate_referential_integrity() ──────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_null(validate_referential_integrity(d)) at test_validate_data.R:259:5
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ecocomDP:::validate_referential_integrity(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─stats::na.omit(data.list[[x]][[primary_key]])
8. ├─data.list[[x]][[primary_key]]
9. └─base::`[[.data.frame`(data.list[[x]], primary_key)
10. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
── Error ('test_validate_data.R:489:5'): validate_data ─────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `.subset2(x, i, exact = exact)`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(validate_data(dataset = d)) at test_validate_data.R:489:5
2. │ └─base::withCallingHandlers(...)
3. └─ecocomDP::validate_data(dataset = d)
4. └─ecocomDP:::validate_primary_keys(d)
5. └─base::lapply(...)
6. └─ecocomDP (local) FUN(X[[i]], ...)
7. ├─data.list[[x]][[primary_key]]
8. └─base::`[[.data.frame`(data.list[[x]], primary_key)
9. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ...
[ FAIL 134 | WARN 3 | SKIP 11 | PASS 467 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘taxize’
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64