Package: atime Check: examples New result: ERROR Running examples in ‘atime-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: references_best > ### Title: Best references > ### Aliases: references_best > > ### ** Examples > > > ## Polynomial and exponential time string functions. > atime_result_string <- atime::atime( + seconds.limit=0.001, + N=unique(as.integer(10^seq(0,4,l=100))), + setup={ + subject <- paste(rep("a", N), collapse="") + pattern <- paste(rep(c("a?", "a"), each=N), collapse="") + linear_size_replacement <- paste(rep("REPLACEMENT", N), collapse="") + }, + PCRE.match=regexpr(pattern, subject, perl=TRUE), + TRE.match=regexpr(pattern, subject, perl=FALSE), + constant.replacement=gsub("a","constant size replacement",subject), + linear.replacement=gsub("a",linear_size_replacement,subject)) > (refs_best_string <- atime::references_best(atime_result_string)) Error in `[.data.table`(all.refs, , `:=`(rank, rank(-N)), by = c(L$by.vec, : attempt access index 6/6 in VECTOR_ELT Calls: -> [ -> [.data.table Execution halted Package: atime Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Custom_Plots.Rmd’ using vignette Quitting from Custom_Plots.Rmd#14-73 [chunk-1] Error: processing vignette 'Custom_Plots.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘Custom_Plots.Rmd’ --- re-building ‘Custom_References.Rmd’ using vignette Quitting from Custom_References.Rmd#70-73 [chunk-2] Error: processing vignette 'Custom_References.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘Custom_References.Rmd’ --- re-building ‘Custom_Units.Rmd’ using vignette Quitting from Custom_Units.Rmd#53-56 [chunk-3] Error: processing vignette 'Custom_Units.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘Custom_Units.Rmd’ --- re-building ‘cum_median.Rmd’ using vignette Quitting from cum_median.Rmd#39-45 [chunk-2] Error: processing vignette 'cum_median.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘cum_median.Rmd’ --- re-building ‘regex.Rmd’ using vignette Quitting from regex.Rmd#31-41 [chunk-3] Error: processing vignette 'regex.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘regex.Rmd’ --- re-building ‘sparse.Rmd’ using vignette Quitting from sparse.Rmd#133-136 [chunk-5] Error: processing vignette 'sparse.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘sparse.Rmd’ SUMMARY: processing the following files failed: ‘Custom_Plots.Rmd’ ‘Custom_References.Rmd’ ‘Custom_Units.Rmd’ ‘cum_median.Rmd’ ‘regex.Rmd’ ‘sparse.Rmd’ Error: Vignette re-building failed. Execution halted Package: atime Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > data.table::setDTthreads(1) # for CRAN. > if(require(testthat))test_check("atime") Loading required package: testthat Loading required package: atime Saving _problems/test-CRAN-75.R Saving _problems/test-CRAN-242.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-CRAN.R:75:3'): more units defined in 1 row result ────────────── Error in ``[.data.table`(all.refs, , `:=`(rank, rank(-N)), by = c(L$by.vec, "fun.name"))`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─atime::references_best(atime.list) at test-CRAN.R:75:3 2. ├─all.refs[, `:=`(rank, rank(-N)), by = c(L$by.vec, "fun.name")] 3. └─data.table:::`[.data.table`(...) ── Error ('test-CRAN.R:242:1'): (code run outside of `test_that()`) ──────────── Error in ``[.data.table`(all.refs, , `:=`(rank, rank(-N)), by = c(L$by.vec, "fun.name"))`: attempt access index 6/6 in VECTOR_ELT Backtrace: ▆ 1. └─atime::references_best(my.atime) at test-CRAN.R:242:1 2. ├─all.refs[, `:=`(rank, rank(-N)), by = c(L$by.vec, "fun.name")] 3. └─data.table:::`[.data.table`(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 17 ] Error: ! Test failures. Execution halted Package: simulist Check: examples New 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 -> -> [ -> [.data.table Execution halted Package: simulist Check: re-building of vignette outputs New 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 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 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 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 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 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 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 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 Package: simulist Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [9s/9s] 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