Last updated on 2025-12-20 11:50:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.1 | 8.77 | 226.56 | 235.33 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.1 | 5.98 | 174.46 | 180.44 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.4.1 | 16.00 | 341.65 | 357.65 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.1 | 15.00 | 346.28 | 361.28 | ERROR | |
| r-devel-windows-x86_64 | 0.4.1 | 11.00 | 260.00 | 271.00 | OK | |
| r-patched-linux-x86_64 | 0.4.1 | 10.56 | 263.62 | 274.18 | OK | |
| r-release-linux-x86_64 | 0.4.1 | 8.40 | 266.57 | 274.97 | OK | |
| r-release-macos-arm64 | 0.4.1 | OK | ||||
| r-release-macos-x86_64 | 0.4.1 | 6.00 | 234.00 | 240.00 | OK | |
| r-release-windows-x86_64 | 0.4.1 | 12.00 | 242.00 | 254.00 | OK | |
| r-oldrel-macos-arm64 | 0.4.1 | OK | ||||
| r-oldrel-macos-x86_64 | 0.4.1 | 6.00 | 222.00 | 228.00 | OK | |
| r-oldrel-windows-x86_64 | 0.4.1 | 14.00 | 318.00 | 332.00 | OK |
Version: 0.4.1
Check: examples
Result: ERROR
Running examples in ‘simDAG-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [65s/95s]
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=1322573 on localhost:11296 at 08:26:05.889
starting worker pid=1322574 on localhost:11296 at 08:26:05.957
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: foreach
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Loading required package: rngtools
Loading required package: foreach
Loading required package: rngtools
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|======================================================================| 100%starting worker pid=1323961 on localhost:11296 at 08:26:08.546
starting worker pid=1323960 on localhost:11296 at 08:26:08.670
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=1325244 on localhost:11296 at 08:26:12.266
starting worker pid=1325243 on localhost:11296 at 08:26:12.298
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
loaded simDAG and set parent environment
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=1327187 on localhost:11296 at 08:26:16.450
starting worker pid=1327188 on localhost:11296 at 08:26:16.536
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Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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
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|======================================================================| 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-linux-x86_64-debian-clang
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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘v_sim_from_dag.Rmd’
--- re-building ‘v_sim_networks.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘v_sim_networks.Rmd’
--- re-building ‘v_using_formulas.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [41s/58s]
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
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|======================================================================| 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-linux-x86_64-debian-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/226s]
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=1850114 on localhost:11216 at 18:32:09.976
starting worker pid=1850115 on localhost:11216 at 18:32:10.115
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loaded simDAG and set parent environment
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: foreach
Attaching package: ‘data.table’
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|======================================================================| 100%starting worker pid=1850863 on localhost:11216 at 18:32:14.917
starting worker pid=1850862 on localhost:11216 at 18:32:14.962
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
loaded simDAG and set parent environment
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=1851815 on localhost:11216 at 18:32:23.488
starting worker pid=1851814 on localhost:11216 at 18:32:23.626
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Loading required package: simDAG
Loading required package: foreach
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=1852710 on localhost:11216 at 18:32:30.916
starting worker pid=1852711 on localhost:11216 at 18:32:31.259
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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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
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
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|======================================================================| 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-linux-x86_64-fedora-clang
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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘v_sim_from_dag.Rmd’
--- re-building ‘v_sim_networks.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘v_sim_networks.Rmd’
--- re-building ‘v_using_formulas.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [102s/184s]
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=280365 on localhost:11485 at 12:53:02.865
starting worker pid=280366 on localhost:11485 at 12:53:03.222
|
| | 0%Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
loaded simDAG and set parent environment
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
|
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|============== | 20%
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|============================ | 40%
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|=================================== | 50%
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|========================================== | 60%
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|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%starting worker pid=280768 on localhost:11485 at 12:53:07.255
starting worker pid=280769 on localhost:11485 at 12:53:07.607
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=281429 on localhost:11485 at 12:53:15.199
starting worker pid=281430 on localhost:11485 at 12:53:15.372
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%
Loading required package: foreach
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
Loading required package: rngtools
starting worker pid=282121 on localhost:11485 at 12:53:22.737
starting worker pid=282122 on localhost:11485 at 12:53:22.808
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
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
|
|=================================== | 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-linux-x86_64-fedora-gcc