Last updated on 2025-12-19 23:50:04 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.0 | 3.19 | 186.16 | 189.35 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.0 | 2.29 | 86.00 | 88.29 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.0 | 201.66 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6.0 | 152.61 | ERROR | |||
| r-devel-windows-x86_64 | 0.6.0 | 8.00 | 231.00 | 239.00 | OK | |
| r-patched-linux-x86_64 | 0.6.0 | 4.47 | 168.13 | 172.60 | OK | |
| r-release-linux-x86_64 | 0.6.0 | 3.15 | 167.56 | 170.71 | OK | |
| r-release-macos-arm64 | 0.6.0 | OK | ||||
| r-release-macos-x86_64 | 0.6.0 | 2.00 | 292.00 | 294.00 | OK | |
| r-release-windows-x86_64 | 0.6.0 | 7.00 | 218.00 | 225.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.6.0 | 2.00 | 335.00 | 337.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.6.0 | 8.00 | 317.00 | 325.00 | NOTE |
Version: 0.6.0
Check: examples
Result: ERROR
Running examples in ‘simulist-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: censor_linelist
> ### Title: Censor dates in line list
> ### Aliases: censor_linelist
>
> ### ** Examples
>
> set.seed(1)
> linelist <- sim_linelist()
Error in `[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, :
attempt access index 3/3 in VECTOR_ELT
Calls: sim_linelist ... .sample_names -> unique -> <Anonymous> -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [14s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(simulist)
>
> test_check("simulist", stop_on_warning = FALSE)
Saving _problems/test-add_cols-187.R
Saving _problems/test-add_cols-200.R
Saving _problems/test-censor_linelist-2.R
Saving _problems/test-messy_linelist-3.R
Saving _problems/test-sim_contacts-3.R
Saving _problems/test-sim_contacts-17.R
Saving _problems/test-sim_contacts-31.R
Saving _problems/test-sim_contacts-45.R
Saving _problems/test-sim_contacts-87.R
Saving _problems/test-sim_linelist-3.R
Saving _problems/test-sim_linelist-25.R
Saving _problems/test-sim_linelist-53.R
Saving _problems/test-sim_linelist-67.R
Saving _problems/test-sim_linelist-85.R
Saving _problems/test-sim_linelist-108.R
Saving _problems/test-sim_linelist-125.R
Saving _problems/test-sim_linelist-159.R
Saving _problems/test-sim_linelist-175.R
Saving _problems/test-sim_linelist-190.R
Saving _problems/test-sim_linelist-249.R
Saving _problems/test-sim_linelist-365.R
Saving _problems/test-sim_linelist-391.R
Saving _problems/test-sim_linelist-419.R
Saving _problems/test-sim_linelist-440.R
Saving _problems/test-sim_outbreak-3.R
Saving _problems/test-sim_outbreak-26.R
Saving _problems/test-sim_outbreak-40.R
Saving _problems/test-sim_outbreak-68.R
Saving _problems/test-sim_outbreak-86.R
Saving _problems/test-truncate_linelist-2.R
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-sim_network_bp.R:4:1', 'test-sim_network_bp.R:17:1',
'test-sim_network_bp.R:31:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-add_cols.R:187:3'): .add_names works as expected ───────────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll) at test-add_cols.R:187:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-add_cols.R:200:3'): .add_names works as expected with anonymise = TRUE ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll, anonymise = TRUE) at test-add_cols.R:200:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-censor_linelist.R:2:1'): (code run outside of `test_that()`) ───
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-censor_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-messy_linelist.R:3:1'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-messy_linelist.R:3:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:3:3'): sim_contacts works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:11:3'): sim_contacts works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:22:3'): sim_contacts works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:36:3'): sim_contacts works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:80:3'): sim_contacts works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:3:3'): sim_linelist works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:17:3'): sim_linelist works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:42:3'): sim_linelist works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:58:3'): sim_linelist works as expected with anonymous ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:76:3'): sim_linelist works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:98:3'): sim_linelist works as expected with age-strat risks & age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:117:3'): sim_linelist gives expected proportion of ages with age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...) at test-sim_linelist.R:117:3
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:148:3'): sim_linelist works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:164:3'): sim_linelist works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:180:3'): sim_linelist warns as expected ─────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:180:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:239:3'): sim_linelist warns when risks are given by onset-to-event is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:239:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:278:3'): sim_linelist is silent when onset is NULL and risk is off ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-sim_linelist.R:278:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simulist::sim_linelist(...)
10. └─simulist:::.sim_internal(...)
11. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
12. └─simulist:::.sample_names(.data = .data)
13. ├─base::unique(...)
14. └─randomNames::randomNames(...)
15. ├─...[]
16. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:357:3'): sim_linest date_admission column is NA when onset_to_hosp is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:357:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:383:3'): sim_linest date_death column is NA when onset_to_death is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:383:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:408:3'): sim_linelist works as expected with time-varying cfr ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:428:3'): sim_linelist works as expected with time-varying cfr & age-strat ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:3:3'): sim_outbreak works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:18:3'): sim_outbreak works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:31:3'): sim_outbreak works as expected with anonymised ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:57:3'): sim_outbreak works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:77:3'): sim_outbreak works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-truncate_linelist.R:2:1'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-truncate_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘age-strat-risks.Rmd’ using rmarkdown
Quitting from age-strat-risks.Rmd:92-103 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'age-strat-risks.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘age-strat-risks.Rmd’
--- re-building ‘age-struct-pop.Rmd’ using rmarkdown
Quitting from age-struct-pop.Rmd:85-96 [sim-linelist-age-range]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'age-struct-pop.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘age-struct-pop.Rmd’
--- re-building ‘design-principles.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘design-principles.Rmd’
--- re-building ‘reporting-delays-truncation.Rmd’ using rmarkdown
Quitting from reporting-delays-truncation.Rmd:87-96 [sim-linelist-no-reporting-delay]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reporting-delays-truncation.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘reporting-delays-truncation.Rmd’
--- re-building ‘simulist.Rmd’ using rmarkdown
Quitting from simulist.Rmd:76-85 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simulist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘simulist.Rmd’
--- re-building ‘time-varying-cfr.Rmd’ using rmarkdown
Quitting from time-varying-cfr.Rmd:108-123 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'time-varying-cfr.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘time-varying-cfr.Rmd’
--- re-building ‘vis-linelist.Rmd’ using rmarkdown
Quitting from vis-linelist.Rmd:76-85 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vis-linelist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘vis-linelist.Rmd’
--- re-building ‘wrangling-linelist.Rmd’ using rmarkdown
Quitting from wrangling-linelist.Rmd:89-99 [sim-outbreak]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'wrangling-linelist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘wrangling-linelist.Rmd’
SUMMARY: processing the following files failed:
‘age-strat-risks.Rmd’ ‘age-struct-pop.Rmd’
‘reporting-delays-truncation.Rmd’ ‘simulist.Rmd’
‘time-varying-cfr.Rmd’ ‘vis-linelist.Rmd’ ‘wrangling-linelist.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
Check: examples
Result: ERROR
Running examples in ‘simulist-Ex.R’ failed
The error most likely occurred in:
> ### Name: censor_linelist
> ### Title: Censor dates in line list
> ### Aliases: censor_linelist
>
> ### ** Examples
>
> set.seed(1)
> linelist <- sim_linelist()
Error in `[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, :
attempt access index 3/3 in VECTOR_ELT
Calls: sim_linelist ... .sample_names -> unique -> <Anonymous> -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [27s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(simulist)
>
> test_check("simulist", stop_on_warning = FALSE)
Saving _problems/test-add_cols-187.R
Saving _problems/test-add_cols-200.R
Saving _problems/test-censor_linelist-2.R
Saving _problems/test-messy_linelist-3.R
Saving _problems/test-sim_contacts-3.R
Saving _problems/test-sim_contacts-17.R
Saving _problems/test-sim_contacts-31.R
Saving _problems/test-sim_contacts-45.R
Saving _problems/test-sim_contacts-87.R
Saving _problems/test-sim_linelist-3.R
Saving _problems/test-sim_linelist-25.R
Saving _problems/test-sim_linelist-53.R
Saving _problems/test-sim_linelist-67.R
Saving _problems/test-sim_linelist-85.R
Saving _problems/test-sim_linelist-108.R
Saving _problems/test-sim_linelist-125.R
Saving _problems/test-sim_linelist-159.R
Saving _problems/test-sim_linelist-175.R
Saving _problems/test-sim_linelist-190.R
Saving _problems/test-sim_linelist-249.R
Saving _problems/test-sim_linelist-365.R
Saving _problems/test-sim_linelist-391.R
Saving _problems/test-sim_linelist-419.R
Saving _problems/test-sim_linelist-440.R
Saving _problems/test-sim_outbreak-3.R
Saving _problems/test-sim_outbreak-26.R
Saving _problems/test-sim_outbreak-40.R
Saving _problems/test-sim_outbreak-68.R
Saving _problems/test-sim_outbreak-86.R
Saving _problems/test-truncate_linelist-2.R
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-sim_network_bp.R:4:1', 'test-sim_network_bp.R:17:1',
'test-sim_network_bp.R:31:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-add_cols.R:187:3'): .add_names works as expected ───────────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll) at test-add_cols.R:187:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-add_cols.R:200:3'): .add_names works as expected with anonymise = TRUE ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll, anonymise = TRUE) at test-add_cols.R:200:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-censor_linelist.R:2:1'): (code run outside of `test_that()`) ───
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-censor_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-messy_linelist.R:3:1'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-messy_linelist.R:3:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:3:3'): sim_contacts works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:11:3'): sim_contacts works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:22:3'): sim_contacts works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:36:3'): sim_contacts works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:80:3'): sim_contacts works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:3:3'): sim_linelist works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:17:3'): sim_linelist works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:42:3'): sim_linelist works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:58:3'): sim_linelist works as expected with anonymous ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:76:3'): sim_linelist works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:98:3'): sim_linelist works as expected with age-strat risks & age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:117:3'): sim_linelist gives expected proportion of ages with age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...) at test-sim_linelist.R:117:3
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:148:3'): sim_linelist works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:164:3'): sim_linelist works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:180:3'): sim_linelist warns as expected ─────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:180:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:239:3'): sim_linelist warns when risks are given by onset-to-event is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:239:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:278:3'): sim_linelist is silent when onset is NULL and risk is off ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-sim_linelist.R:278:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simulist::sim_linelist(...)
10. └─simulist:::.sim_internal(...)
11. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
12. └─simulist:::.sample_names(.data = .data)
13. ├─base::unique(...)
14. └─randomNames::randomNames(...)
15. ├─...[]
16. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:357:3'): sim_linest date_admission column is NA when onset_to_hosp is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:357:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:383:3'): sim_linest date_death column is NA when onset_to_death is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:383:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:408:3'): sim_linelist works as expected with time-varying cfr ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:428:3'): sim_linelist works as expected with time-varying cfr & age-strat ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:3:3'): sim_outbreak works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:18:3'): sim_outbreak works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:31:3'): sim_outbreak works as expected with anonymised ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:57:3'): sim_outbreak works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:77:3'): sim_outbreak works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-truncate_linelist.R:2:1'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-truncate_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘age-strat-risks.Rmd’ using rmarkdown
Quitting from age-strat-risks.Rmd:92-103 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'age-strat-risks.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘age-strat-risks.Rmd’
--- re-building ‘age-struct-pop.Rmd’ using rmarkdown
Quitting from age-struct-pop.Rmd:85-96 [sim-linelist-age-range]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'age-struct-pop.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘age-struct-pop.Rmd’
--- re-building ‘design-principles.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘design-principles.Rmd’
--- re-building ‘reporting-delays-truncation.Rmd’ using rmarkdown
Quitting from reporting-delays-truncation.Rmd:87-96 [sim-linelist-no-reporting-delay]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reporting-delays-truncation.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘reporting-delays-truncation.Rmd’
--- re-building ‘simulist.Rmd’ using rmarkdown
Quitting from simulist.Rmd:76-85 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simulist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘simulist.Rmd’
--- re-building ‘time-varying-cfr.Rmd’ using rmarkdown
Quitting from time-varying-cfr.Rmd:108-123 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'time-varying-cfr.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘time-varying-cfr.Rmd’
--- re-building ‘vis-linelist.Rmd’ using rmarkdown
Quitting from vis-linelist.Rmd:76-85 [sim-linelist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vis-linelist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘vis-linelist.Rmd’
--- re-building ‘wrangling-linelist.Rmd’ using rmarkdown
Quitting from wrangling-linelist.Rmd:89-99 [sim-outbreak]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'wrangling-linelist.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘wrangling-linelist.Rmd’
SUMMARY: processing the following files failed:
‘age-strat-risks.Rmd’ ‘age-struct-pop.Rmd’
‘reporting-delays-truncation.Rmd’ ‘simulist.Rmd’
‘time-varying-cfr.Rmd’ ‘vis-linelist.Rmd’ ‘wrangling-linelist.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [47s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(simulist)
>
> test_check("simulist", stop_on_warning = FALSE)
Saving _problems/test-add_cols-187.R
Saving _problems/test-add_cols-200.R
Saving _problems/test-censor_linelist-2.R
Saving _problems/test-messy_linelist-3.R
Saving _problems/test-sim_contacts-3.R
Saving _problems/test-sim_contacts-17.R
Saving _problems/test-sim_contacts-31.R
Saving _problems/test-sim_contacts-45.R
Saving _problems/test-sim_contacts-87.R
Saving _problems/test-sim_linelist-3.R
Saving _problems/test-sim_linelist-25.R
Saving _problems/test-sim_linelist-53.R
Saving _problems/test-sim_linelist-67.R
Saving _problems/test-sim_linelist-85.R
Saving _problems/test-sim_linelist-108.R
Saving _problems/test-sim_linelist-125.R
Saving _problems/test-sim_linelist-159.R
Saving _problems/test-sim_linelist-175.R
Saving _problems/test-sim_linelist-190.R
Saving _problems/test-sim_linelist-249.R
Saving _problems/test-sim_linelist-365.R
Saving _problems/test-sim_linelist-391.R
Saving _problems/test-sim_linelist-419.R
Saving _problems/test-sim_linelist-440.R
Saving _problems/test-sim_outbreak-3.R
Saving _problems/test-sim_outbreak-26.R
Saving _problems/test-sim_outbreak-40.R
Saving _problems/test-sim_outbreak-68.R
Saving _problems/test-sim_outbreak-86.R
Saving _problems/test-truncate_linelist-2.R
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-sim_network_bp.R:4:1', 'test-sim_network_bp.R:17:1',
'test-sim_network_bp.R:31:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-add_cols.R:187:3'): .add_names works as expected ───────────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll) at test-add_cols.R:187:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-add_cols.R:200:3'): .add_names works as expected with anonymise = TRUE ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist:::.add_names(.data = ll, anonymise = TRUE) at test-add_cols.R:200:3
2. └─simulist:::.sample_names(.data = .data)
3. ├─base::unique(...)
4. └─randomNames::randomNames(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-censor_linelist.R:2:1'): (code run outside of `test_that()`) ───
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-censor_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-messy_linelist.R:3:1'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-messy_linelist.R:3:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:3:3'): sim_contacts works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:11:3'): sim_contacts works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:22:3'): sim_contacts works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:36:3'): sim_contacts works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_contacts.R:80:3'): sim_contacts works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_contacts(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:3:3'): sim_linelist works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:17:3'): sim_linelist works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:42:3'): sim_linelist works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:58:3'): sim_linelist works as expected with anonymous ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:76:3'): sim_linelist works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:98:3'): sim_linelist works as expected with age-strat risks & age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:117:3'): sim_linelist gives expected proportion of ages with age struct ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...) at test-sim_linelist.R:117:3
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:148:3'): sim_linelist works as expected with modified config ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:164:3'): sim_linelist works as expected with modified config parameters ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:180:3'): sim_linelist warns as expected ─────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:180:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:239:3'): sim_linelist warns when risks are given by onset-to-event is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-sim_linelist.R:239:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─simulist::sim_linelist(...)
8. └─simulist:::.sim_internal(...)
9. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
10. └─simulist:::.sample_names(.data = .data)
11. ├─base::unique(...)
12. └─randomNames::randomNames(...)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:278:3'): sim_linelist is silent when onset is NULL and risk is off ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-sim_linelist.R:278:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simulist::sim_linelist(...)
10. └─simulist:::.sim_internal(...)
11. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
12. └─simulist:::.sample_names(.data = .data)
13. ├─base::unique(...)
14. └─randomNames::randomNames(...)
15. ├─...[]
16. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:357:3'): sim_linest date_admission column is NA when onset_to_hosp is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:357:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:383:3'): sim_linest date_death column is NA when onset_to_death is NULL ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-sim_linelist.R:383:3
2. │ └─base::withCallingHandlers(...)
3. └─simulist::sim_linelist(...)
4. └─simulist:::.sim_internal(...)
5. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
6. └─simulist:::.sample_names(.data = .data)
7. ├─base::unique(...)
8. └─randomNames::randomNames(...)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:408:3'): sim_linelist works as expected with time-varying cfr ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_linelist.R:428:3'): sim_linelist works as expected with time-varying cfr & age-strat ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:3:3'): sim_outbreak works as expected with defaults ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak()
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:18:3'): sim_outbreak works as expected ──────────
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:31:3'): sim_outbreak works as expected with anonymised ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:57:3'): sim_outbreak works as expected with age-strat risks ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-sim_outbreak.R:77:3'): sim_outbreak works as expected with age structure ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_outbreak(...)
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-truncate_linelist.R:2:1'): (code run outside of `test_that()`) ──
Error in ``[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender, ethnicity, .N)), by = list(gender, ethnicity))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simulist::sim_linelist() at test-truncate_linelist.R:2:1
2. └─simulist:::.sim_internal(...)
3. └─simulist:::.add_names(.data = .data, anonymise = anonymise)
4. └─simulist:::.sample_names(.data = .data)
5. ├─base::unique(...)
6. └─randomNames::randomNames(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 31 | WARN 1 | SKIP 3 | PASS 139 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6.0
Check: installed package size
Result: NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 6.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64