Last updated on 2025-12-28 01:49:19 CET.
| Package | ERROR | OK |
|---|---|---|
| adjustedCurves | 13 | |
| CareDensity | 13 | |
| contsurvplot | 13 | |
| simDAG | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 0.4.1
Check: examples
Result: ERROR
Running examples in 'simDAG-Ex.R' failed
The error most likely occurred in:
> ### Name: long2start_stop
> ### Title: Transform a 'data.table' in the long-format to a 'data.table' in
> ### the start-stop format
> ### Aliases: long2start_stop
>
> ### ** Examples
>
> library(simDAG)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
>
> # generate example data in long format
> long <- data.table(.id=rep(seq_len(10), each=5),
+ .time=rep(seq_len(5), 10),
+ A=c(rep(FALSE, 43), TRUE, TRUE, rep(FALSE, 3), TRUE,
+ TRUE),
+ B=FALSE)
> setkey(long, .id, .time)
>
> # transform to start-stop format
> long2start_stop(data=long, id=".id", time=".time", varying=c("A", "B"))
Error in `[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), :
attempt access index 4/4 in VECTOR_ELT
Calls: long2start_stop -> [ -> [.data.table
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.4.1
Check: tests
Result: ERROR
Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> library(igraph)
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
>
> data.table::setDTthreads(1)
>
> test_check("simDAG")
Saving _problems/test_collapse_for_target_event-19.R
Saving _problems/test_collapse_for_target_event-32.R
Saving _problems/test_collapse_for_target_event-45.R
Saving _problems/test_collapse_for_target_event-66.R
Saving _problems/test_collapse_for_target_event-86.R
Saving _problems/test_collapse_for_target_event-98.R
Saving _problems/test_collapse_for_target_event-117.R
Saving _problems/test_collapse_for_target_event-136.R
Saving _problems/test_collapse_for_target_event-147.R
Saving _problems/test_collapse_for_target_event-164.R
Saving _problems/test_collapse_for_target_event-184.R
Saving _problems/test_dag_from_data-134.R
Saving _problems/test_input_checks_sim2data-80.R
Saving _problems/test_input_checks_sim2data-92.R
Saving _problems/test_long2start_stop-18.R
Saving _problems/test_long2start_stop-45.R
Saving _problems/test_long2start_stop-66.R
Saving _problems/test_long2start_stop-87.R
Saving _problems/test_long2start_stop-110.R
Saving _problems/test_long2start_stop-130.R
Saving _problems/test_network-327.R
Saving _problems/test_node_time_to_event-170.R
Saving _problems/test_remove_not_at_risk-17.R
Saving _problems/test_remove_not_at_risk-39.R
Saving _problems/test_remove_not_at_risk-58.R
Saving _problems/test_remove_vars_simDT-22.R
Saving _problems/test_remove_vars_simDT-34.R
Saving _problems/test_sim2data-31.R
Saving _problems/test_sim2data-43.R
Saving _problems/test_sim2data-54.R
Saving _problems/test_sim2data-65.R
Saving _problems/test_sim2data-94.R
Saving _problems/test_sim2data_all_equal_last-23.R
Saving _problems/test_sim2data_all_equal_last-32.R
Saving _problems/test_sim2long.last-32.R
Saving _problems/test_sim2long.last-74.R
Saving _problems/test_sim2start_stop.all-19.R
Saving _problems/test_sim2start_stop.all-51.R
Saving _problems/test_sim2start_stop.last-53.R
Saving _problems/test_sim2start_stop.last-105.R
Saving _problems/test_sim2start_stop.last-138.R
Saving _problems/test_sim2start_stop.last-171.R
Saving _problems/test_sim2start_stop.last-203.R
Saving _problems/test_sim2start_stop.last-235.R
Saving _problems/test_sim2start_stop.last-268.R
Saving _problems/test_sim2start_stop.last-300.R
Saving _problems/test_sim2start_stop.last-359.R
t = 1 node = sickness2
t = 1 node = sickness1
t = 2 node = sickness2
t = 2 node = sickness1
t = 3 node = sickness2
t = 3 node = sickness1
t = 4 node = sickness2
t = 4 node = sickness1
t = 5 node = sickness2
t = 5 node = sickness1
Saving _problems/test_sim_n_datasets-38.R
starting worker pid=53816 on localhost:11699 at 20:32:47.104
starting worker pid=53836 on localhost:11699 at 20:32:47.105
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
Loading required package: simDAG
The following object is masked from 'package:base':
%notin%
loaded simDAG and set parent environment
Loading required package: foreach
Attaching package: 'data.table'
Loading required package: rngtools
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%starting worker pid=92356 on localhost:11699 at 20:32:48.506
starting worker pid=17928 on localhost:11699 at 20:32:48.535
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
Loading required package: simDAG
loaded simDAG and set parent environment
The following object is masked from 'package:base':
%notin%
Attaching package: 'data.table'
Loading required package: foreach
Loading required package: rngtools
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
starting worker pid=53280 on localhost:11699 at 20:32:50.429
starting worker pid=93440 on localhost:11699 at 20:32:50.439
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
starting worker pid=70884 on localhost:11699 at 20:32:52.408
starting worker pid=25140 on localhost:11699 at 20:32:52.420
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%[ FAIL 48 | WARN 14 | SKIP 54 | PASS 818 ]
══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On CRAN (54): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_plot.DAG.r:11:1',
'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1', 'test_plot.DAG.r:23:1',
'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1', 'test_plot.DAG.r:35:1',
'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1', 'test_plot.DAG.r:52:1',
'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1', 'test_plot.DAG.r:69:1',
'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1', 'test_plot.DAG.r:108:1',
'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1', 'test_plot.simDT.r:32:1',
'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1', 'test_plot.simDT.r:48:1',
'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1', 'test_simDT_S3.r:15:1',
'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_collapse_for_target_event.r:19:3'): standard should be shortened ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:19:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:32:3'): standard should not be shortened ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:32:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:45:3'): event at the start ─────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:45:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:66:3'): event at the end ───────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:66:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:86:3'): multiple events per person that should be shortened ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, target_event = "target") at test_collapse_for_target_event.r:86:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:98:3'): multiple events per person that should not be shortened ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, target_event = "target") at test_collapse_for_target_event.r:98:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:117:3'): two events right after each other ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:117:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:136:3'): three events right after each other ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, "target") at test_collapse_for_target_event.r:136:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:147:3'): one event starting right after it ends, with no event to shorten ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, target_event = "C") at test_collapse_for_target_event.r:147:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:164:3'): one event starting right after it ends, with one event to shorten ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(d_test, target_event = "C") at test_collapse_for_target_event.r:164:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_collapse_for_target_event.r:183:3'): only keeping time to first event ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = .id, .SDcols = setdiff(names(data), c(".id", "start", "stop", target_event)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::collapse_for_target_event(...) at test_collapse_for_target_event.r:183:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_dag_from_data.r:133:3'): gen_node_conditional_prob ─────────────
Error in ``[.data.table`(data, , `:=`(prob, mean(eval(parse(text = name)), na.rm = na.rm)), by = ..interact_parents..)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::gen_node_conditional_prob(...) at test_dag_from_data.r:133:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_input_checks_sim2data.r:80:3'): warning save_states='at_t' ─────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(sim2data(sim, to = "long")) at test_input_checks_sim2data.r:80:3
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. └─simDAG::sim2data(sim, to = "long")
8. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
9. └─simDAG:::sim2long.last(sim = sim)
10. └─simDAG:::sim2start_stop.last(sim)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test_input_checks_sim2data.r:92:19'): warning with potentially incorrect output for variables ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_input_checks_sim2data.r:92:3
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. └─simDAG::sim2data(sim, to = "long") at test_input_checks_sim2data.r:92:19
8. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
9. └─simDAG:::sim2long.last(sim = sim)
10. └─simDAG:::sim2start_stop.last(sim)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:17:3'): general test case ────────────────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:17:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:44:3'): shuffled input ───────────────────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:44:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:65:3'): event right at the end ───────────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:65:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:86:3'): event right at the start ─────────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:86:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:109:3'): event of length 1 right at the start ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:109:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_long2start_stop.r:129:3'): non-logical time-varying variables ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::long2start_stop(...) at test_long2start_stop.r:129:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_network.r:327:3'): static network with discrete-time simulation ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop") at test_network.r:327:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.all(...)
4. └─simDAG::long2start_stop(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_node_time_to_event.r:170:3'): using the 'unif' argument ────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop") at test_node_time_to_event.r:170:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_remove_not_at_risk.r:16:3'): general test case, no overlap ─────
Error in ``[.data.table`(data, , `:=`(.last_event, na_locf(fifelse(eval(parse(text = target_event)) == TRUE, stop, NA))), by = .id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::remove_not_at_risk(...) at test_remove_not_at_risk.r:16:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_remove_not_at_risk.r:38:3'): general test case, with overlap ───
Error in ``[.data.table`(data, , `:=`(.last_event, na_locf(fifelse(eval(parse(text = target_event)) == TRUE, stop, NA))), by = .id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::remove_not_at_risk(...) at test_remove_not_at_risk.r:38:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_remove_not_at_risk.r:57:3'): events right after each other ─────
Error in ``[.data.table`(data, , `:=`(.last_event, na_locf(fifelse(eval(parse(text = target_event)) == TRUE, stop, NA))), by = .id)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::remove_not_at_risk(...) at test_remove_not_at_risk.r:57:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_remove_vars_simDT.r:22:3'): removing only a constant variable ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop", remove_vars = "F") at test_remove_vars_simDT.r:22:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.all(...)
4. └─simDAG::long2start_stop(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_remove_vars_simDT.r:34:3'): removing other variables ───────────
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop", remove_vars = rm_vars) at test_remove_vars_simDT.r:34:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.all(...)
4. └─simDAG::long2start_stop(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data.r:31:3'): as start_stop data ──────────────────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim = sim, to = "start_stop") at test_sim2data.r:31:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data.r:43:3'): as long data ────────────────────────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim = sim, to = "long") at test_sim2data.r:43:3
2. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
3. └─simDAG:::sim2long.last(sim = sim)
4. └─simDAG:::sim2start_stop.last(sim)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data.r:54:3'): as wide data ────────────────────────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim = sim, to = "wide") at test_sim2data.r:54:3
2. └─simDAG:::sim2wide(sim = sim, use_saved_states = use_saved_states)
3. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
4. └─simDAG:::sim2long.last(sim = sim)
5. └─simDAG:::sim2start_stop.last(sim)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data.r:65:3'): as start_stop data, with data.frame output ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim = sim, to = "start_stop", as_data_frame = TRUE) at test_sim2data.r:65:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data.r:94:3'): as wide data, with multiple time-varying variables ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "wide") at test_sim2data.r:94:3
2. └─simDAG:::sim2wide(sim = sim, use_saved_states = use_saved_states)
3. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
4. └─simDAG:::sim2long.last(sim = sim)
5. └─simDAG:::sim2start_stop.last(sim)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data_all_equal_last.r:23:3'): start-stop: .all equal to .last ──
Error in ``[.data.table`(data, , `:=`(.is_equal_to_next, check_next_row_equal(.SD)), by = "..id..", .SDcols = varying)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop", use_saved_states = TRUE) at test_sim2data_all_equal_last.r:23:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.all(...)
4. └─simDAG::long2start_stop(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_sim2data_all_equal_last.r:32:3'): long: .all equal to .last ────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "long", use_saved_states = FALSE) at test_sim2data_all_equal_last.r:32:3
2. └─simDAG:::sim2long(sim = sim, use_saved_states = use_saved_states)
3. └─simDAG:::sim2long.last(sim = sim)
4. └─simDAG:::sim2start_stop.last(sim)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test_sim2long.last.r:32:3'): general test case ──────────────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2long.last(sim) at test_sim2long.last.r:32:3
2. └─simDAG:::sim2start_stop.last(sim)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_sim2long.last.r:74:3'): adding time_since_last and event_count afterwards ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2long.last(sim) at test_sim2long.last.r:74:3
2. └─simDAG:::sim2start_stop.last(sim)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.all.r:18:3'): outcome centric with event_duration > 1 ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(...) at test_sim2start_stop.all.r:18:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.all.r:50:3'): outcome centric with event_duration == 1 ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim2data(...) at test_sim2start_stop.all.r:50:3
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:53:3'): overall test case 1 time_to_event node ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:53:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:105:3'): overall test case 3 time_to_event nodes ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:105:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:138:3'): two events stopping at the same time ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:138:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:171:3'): two events starting at the same time ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:171:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:203:3'): one event starting when other ends ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:203:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:235:3'): one event starting one t before other ends ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:235:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:268:3'): event starting right when the same event just ended ──
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:268:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:300:3'): node containing no events ───────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:300:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim2start_stop.last.r:359:3'): event at t = max_t ──────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG:::sim2start_stop.last(sim) at test_sim2start_stop.last.r:359:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test_sim_n_datasets.r:37:3'): with td, data_format ──────────────────
Error in ``[.data.table`(data, , `:=`(stop, shift(start, type = "lead", fill = max_t + 1)), by = .id)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simDAG::sim_n_datasets(...) at test_sim_n_datasets.r:37:3
2. └─simDAG:::generate_one_dataset(...)
3. ├─base::do.call("sim2data", args = data_format_args)
4. └─simDAG::sim2data(to = "start_stop", sim = `<simDT>`)
5. └─simDAG:::sim2start_stop(...)
6. └─simDAG:::sim2start_stop.last(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 48 | WARN 14 | SKIP 54 | PASS 818 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'simDAG.Rmd' using rmarkdown
Quitting from simDAG.Rmd:444-448 [unnamed-chunk-23]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simDAG::sim2data(...)
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simDAG.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building 'simDAG.Rmd'
--- re-building 'v_cookbook.Rmd' using rmarkdown
Quitting from v_cookbook.Rmd:173-198 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop", overlap = TRUE)
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'v_cookbook.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building 'v_cookbook.Rmd'
--- re-building 'v_covid_example.Rmd' using rmarkdown
Quitting from v_covid_example.Rmd:226-228 [unnamed-chunk-12]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simDAG::sim2data(sim, to = "start_stop")
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'v_covid_example.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building 'v_covid_example.Rmd'
--- re-building 'v_custom_nodes.Rmd' using rmarkdown
--- finished re-building 'v_custom_nodes.Rmd'
--- re-building 'v_sim_discrete_time.Rmd' using rmarkdown
Quitting from v_sim_discrete_time.Rmd:174-177 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simDAG::sim2data(sim_dat, to = "start_stop")
2. └─simDAG:::sim2start_stop(...)
3. └─simDAG:::sim2start_stop.last(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'v_sim_discrete_time.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building 'v_sim_discrete_time.Rmd'
--- re-building 'v_sim_from_dag.Rmd' using rmarkdown
--- finished re-building 'v_sim_from_dag.Rmd'
--- re-building 'v_sim_networks.Rmd' using rmarkdown
--- finished re-building 'v_sim_networks.Rmd'
--- re-building 'v_using_formulas.Rmd' using rmarkdown
--- finished re-building 'v_using_formulas.Rmd'
SUMMARY: processing the following files failed:
'simDAG.Rmd' 'v_cookbook.Rmd' 'v_covid_example.Rmd'
'v_sim_discrete_time.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.