• using R Under development (unstable) (2025-12-19 r89206)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘simulist/DESCRIPTION’ ... OK
• this is package ‘simulist’ version ‘0.6.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘simulist’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [4s/6s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/16s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [14s/16s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [41s/52s] 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
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [4s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs