Last updated on 2025-12-20 17:50:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.2 | 21.26 | 274.01 | 295.27 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 14.53 | 172.87 | 187.40 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 43.00 | 448.04 | 491.04 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 40.00 | 425.40 | 465.40 | ERROR | |
| r-devel-windows-x86_64 | 1.0.2 | 29.00 | 514.00 | 543.00 | OK | |
| r-patched-linux-x86_64 | 1.0.2 | 22.53 | 477.92 | 500.45 | OK | |
| r-release-linux-x86_64 | 1.0.2 | 21.69 | 480.10 | 501.79 | OK | |
| r-release-macos-arm64 | 1.0.2 | 5.00 | 125.00 | 130.00 | OK | |
| r-release-macos-x86_64 | 1.0.2 | 15.00 | 636.00 | 651.00 | OK | |
| r-release-windows-x86_64 | 1.0.2 | 29.00 | 503.00 | 532.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.2 | 5.00 | 126.00 | 131.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.2 | 16.00 | 716.00 | 732.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.2 | 32.00 | 682.00 | 714.00 | OK |
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘simtrial-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_gt
> ### Title: Convert summary table to a gt object
> ### Aliases: as_gt as_gt.simtrial_gs_wlr
>
> ### ** Examples
>
>
> # Parameters for enrollment
> enroll_rampup_duration <- 4 # Duration for enrollment ramp up
> enroll_duration <- 16 # Total enrollment duration
> enroll_rate <- gsDesign2::define_enroll_rate(
+ duration = c(
+ enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
+ rate = c(10, 30))
>
> # Parameters for treatment effect
> delay_effect_duration <- 3 # Delay treatment effect in months
> median_ctrl <- 9 # Survival median of the control arm
> median_exp <- c(9, 14) # Survival median of the experimental arm
> dropout_rate <- 0.001
> fail_rate <- gsDesign2::define_fail_rate(
+ duration = c(delay_effect_duration, 100),
+ fail_rate = log(2) / median_ctrl,
+ hr = median_ctrl / median_exp,
+ dropout_rate = dropout_rate)
>
> # Other related parameters
> alpha <- 0.025 # Type I error
> beta <- 0.1 # Type II error
> ratio <- 1 # Randomization ratio (experimental:control)
>
> # Build a one-sided group sequential design
> design <- gsDesign2::gs_design_ahr(
+ enroll_rate = enroll_rate, fail_rate = fail_rate,
+ ratio = ratio, alpha = alpha, beta = beta,
+ analysis_time = c(12, 24, 36),
+ upper = gsDesign2::gs_spending_bound,
+ upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
+ lower = gsDesign2::gs_b,
+ lpar = rep(-Inf, 3))
Error in `[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time)) :
attempt access index 6/6 in VECTOR_ELT
Calls: <Anonymous> ... gs_info_ahr -> select -> ahr -> pw_info -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [143s/256s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simtrial)
>
> test_check("simtrial")
Saving _problems/test-developer-get_analysis_date-18.R
Saving _problems/test-developer-get_analysis_date-61.R
Saving _problems/test-double_programming_mb_weight-21.R
Saving _problems/test-double_programming_mb_weight-52.R
Saving _problems/test-double_programming_mb_weight-83.R
Saving _problems/test-double_programming_sim_fixed_n-44.R
Saving _problems/test-double_programming_sim_pw_surv-5.R
Saving _problems/test-double_programming_sim_pw_surv-19.R
Saving _problems/test-double_programming_sim_pw_surv-28.R
Saving _problems/test-double_programming_sim_pw_surv-36.R
Saving _problems/test-double_programming_sim_pw_surv-49.R
Saving _problems/test-double_programming_sim_pw_surv-64.R
Saving _problems/test-independent_test_counting_process-12.R
Saving _problems/test-independent_test_counting_process-32.R
Saving _problems/test-independent_test_cut_data_by_date-2.R
Saving _problems/test-independent_test_cut_data_by_date-16.R
Saving _problems/test-independent_test_cut_data_by_date-27.R
Saving _problems/test-independent_test_cut_data_by_date-37.R
Saving _problems/test-independent_test_cut_data_by_event-2.R
Saving _problems/test-independent_test_early_zero_weight-8.R
Saving _problems/test-independent_test_early_zero_weight-41.R
Saving _problems/test-independent_test_early_zero_weight-95.R
Saving _problems/test-independent_test_early_zero_weight-148.R
Saving _problems/test-independent_test_fh_weight-5.R
Saving _problems/test-independent_test_fh_weight-36.R
Saving _problems/test-independent_test_get_cut_date_by_event-5.R
Saving _problems/test-independent_test_pvalue_maxcombo-7.R
Saving _problems/test-independent_test_simfix2simpwsurv-2.R
Saving _problems/test-independent_test_simfix2simpwsurv-21.R
Saving _problems/test-independent_test_simfix2simpwsurv-35.R
Saving _problems/test-independent_test_simfix2simpwsurv-45.R
Saving _problems/test-independent_test_simfix2simpwsurv-54.R
Saving _problems/test-independent_test_simfix2simpwsurv-64.R
Saving _problems/test-independent_test_simfix2simpwsurv-75.R
Saving _problems/test-independent_test_simfix2simpwsurv-83.R
Saving _problems/test-independent_test_simfix2simpwsurv-91.R
Saving _problems/test-independent_test_simfix2simpwsurv-98.R
Saving _problems/test-independent_test_wlr-7.R
Saving _problems/test-independent_test_wlr-55.R
Saving _problems/test-independent_test_wlr-90.R
Saving _problems/test-independent_test_wlr-144.R
Saving _problems/test-independent_test_wlr-186.R
Saving _problems/test-independent_test_wlr-233.R
Saving _problems/test-unvalidated-data.table-11.R
Saving _problems/test-unvalidated-data.table-70.R
Saving _problems/test-unvalidated-early_zero_weight-8.R
Saving _problems/test-unvalidated-early_zero_weight-43.R
Saving _problems/test-unvalidated-early_zero_weight-92.R
Saving _problems/test-unvalidated-get_analysis_date-4.R
Saving _problems/test-unvalidated-get_analysis_date-12.R
Saving _problems/test-unvalidated-get_analysis_date-20.R
Saving _problems/test-unvalidated-get_analysis_date-32.R
Saving _problems/test-unvalidated-get_analysis_date-43.R
Saving _problems/test-unvalidated-get_analysis_date-55.R
Saving _problems/test-unvalidated-get_analysis_date-67.R
Saving _problems/test-unvalidated-get_analysis_date-81.R
Saving _problems/test-unvalidated-get_analysis_date-93.R
Saving _problems/test-unvalidated-get_analysis_date-105.R
Saving _problems/test-unvalidated-get_analysis_date-120.R
Saving _problems/test-unvalidated-maxcombo-8.R
Saving _problems/test-unvalidated-maxcombo-14.R
Saving _problems/test-unvalidated-multitest-2.R
Backend uses sequential processing.
Saving _problems/test-unvalidated-sim_gs_n-84.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-125.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-166.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-206.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-246.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-285.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-324.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-365.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-413.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-455.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-513.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-529.R
Saving _problems/test-unvalidated-sim_gs_n-625.R
Saving _problems/test-unvalidated-sim_gs_n-668.R
Saving _problems/test-unvalidated-sim_gs_n-734.R
Saving _problems/test-unvalidated-summary-36.R
Saving _problems/test-unvalidated-summary-126.R
Saving _problems/test-unvalidated-wlr-3.R
Saving _problems/test-unvalidated-wlr-35.R
Saving _problems/test-unvalidated-wlr-49.R
Saving _problems/test-unvalidated-wlr-55.R
Saving _problems/test-unvalidated-wlr-63.R
Saving _problems/test-unvalidated-wlr-91.R
Saving _problems/test-unvalidated-wlr-123.R
Saving _problems/test-unvalidated-wlr-136.R
Saving _problems/test-unvalidated-wlr-150.R
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-developer-get_analysis_date.R:2:3'): Cut by targeted event per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-developer-get_analysis_date.R:45:3'): Cut by targeted sample size per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:45:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:19:3'): mb_weight works for single stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:19:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(n = 200)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:32:3'): mb_weight works for multiple strata ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:32:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:63:3'): mb_weight works for a stratum with no records before delay ends ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:63:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_fixed_n.R:24:3'): Double programming of sim_fixed_n ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...) at test-double_programming_sim_fixed_n.R:24:3
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:5:3'): stratum percentage calculated from simulated dataset must be within
the tolerance=0.002 of stratum in setup (0.4,0.6) ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:5:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:19:3'): block calculated from simulated dataset equals size of 4 with 1:1
randomization, which is 2 for each arm ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:19:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:28:3'): fail_rate calculated from simulated dataset must be within the
tolerance=0.1 of fail_rate in setting ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:28:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:36:3'): dropout_rate calculated from simulated dataset must be within
the tolerance=0.0005 of dropout_rate=0.001 in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:36:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:49:3'): enroll_rate calculated from simulated dataset must be within
the relative tolerance=0.05 of enroll_rate in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:49:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:64:3'): The actual number of events changes by changing total sample size ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:64:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:90:3'): sim_pw_surv() fails early with mismatched treatment names ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-double_programming_sim_pw_surv.R:90:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simtrial::sim_pw_surv(block = block, fail_rate = fail_rate, dropout_rate = dropout_rate)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:12:3'): Counting Process Format without ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:12:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:32:3'): Counting Process Format with ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:32:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:2:3'): x is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:16:3'): only patients recorded by cut_data_by_date are included ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:16:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:27:3'): Time-to-event (TTE) is cut off at the cut_date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:27:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:37:3'): the event variable is calculated correctly ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:37:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_event.R:2:3'): the input is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_event.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-independent_test_early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:41:3'): early_zero_weight() with stratified data when fail_rate is not provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:41:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:95:3'): early_zero_weight() with stratified data when fail_rate is not correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:95:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:148:3'): early_zero_weight() with stratified data when fail_rate is correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:148:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:5:3'): the z values match with the correspondings in fh_weight ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:5:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:36:3'): fh_weight calculated correct correlation value when input a sequence of rho and gamma ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:36:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_get_cut_date_by_event.R:5:3'): get_cut_date_by_event returns the correct cut date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_get_cut_date_by_event.R:5:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_pvalue_maxcombo.R:7:3'): the p-values correspond to pvalue_maxcombo ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_pvalue_maxcombo.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:2:3'): stratum values must be the same and stratum length must be doubled after converting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:2:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:21:3'): treatment after converting contains only control and experimental with the right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:21:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:35:3'): Duration values match before and after converting and in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:35:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:45:3'): fail_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:45:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:54:3'): dropout_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:54:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:64:3'): fail_rate column names must contain stratum, duration, fail_rate, hr and dropout_rate ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:64:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:75:3'): duration must be longer than 0 ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:75:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:83:3'): fail_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:83:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:91:3'): hr must be postiive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:91:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:98:3'): dropout_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:98:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:7:3'): wlr() with FH weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:55:3'): wlr() with FH weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:90:3'): wlr() with MB weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:90:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:144:3'): wlr() with MB weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:144:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:186:3'): wlr() with early_zero_weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:186:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:233:3'): wlr() with early_zero_weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:233:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:11:3'): functions that use data.table still return a data frame ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-unvalidated-data.table.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simtrial::counting_process(x, arm = 1)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:70:3'): functions that use data.table do not modify input data table ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm = 1) at test-unvalidated-data.table.R:70:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-unvalidated-early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:43:3'): early_zero_weight() with stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:43:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:92:3'): early_zero_weight() fails with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:92:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:4:3'): planned_calendar_time ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:4:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:12:3'): target_event_overall ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:12:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:20:3'): planned_calendar_time + target_event_overall ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:20:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:32:3'): target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:32:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:43:3'): target_event_overall + target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:43:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:55:3'): target_event_per_stratum + max_extension_for_target_event ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:55:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:67:3'): min_n_overall + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:67:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:81:3'): min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:81:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:93:3'): min_n_per_stratum + min_followup (requirement for only one stratum) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:93:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:105:3'): min_n_overall + min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:105:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:120:3'): get_analysis_date() fails early with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:120:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:6:3'): maxcombo returns consistent results ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::maxcombo(...) at test-unvalidated-maxcombo.R:6:3
2. │ └─simtrial::counting_process(data, arm = "experimental")
3. │ └─base::unique(x$treatment)
4. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150)
5. │ └─simtrial::get_cut_date_by_event(x, event)
6. │ └─data.table::as.data.table(x)
7. └─simtrial::sim_pw_surv(n = 200)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:14:3'): maxcombo fails early with bad input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150) at test-unvalidated-maxcombo.R:14:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-multitest.R:2:3'): multitest() is equivalent to running tests individually ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-unvalidated-multitest.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:75:3'): regular logrank test ────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:75:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:116:3'): regular logrank test parallel ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:116:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:157:3'): weighted logrank test by FH(0, 0.5) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:157:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:197:3'): weighted logrank test by MB(3) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:197:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:237:3'): weighted logrank test by early zero (6) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:237:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:277:3'): RMST ───────────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:277:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:315:3'): Milestone ──────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:315:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:358:3'): WLR with fh(0, 0.5) test at IA1, WLR with mb(6, Inf) at IA2, and milestone test at FA ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:358:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:404:3'): MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5)) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:404:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:448:3'): sim_gs_n() accepts different tests per cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:448:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:503:3'): sim_gs_n() requires a test for each cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-unvalidated-sim_gs_n.R:503:3
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. └─simtrial::sim_gs_n(...)
8. └─... %dofuture% ...
9. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(...)
13. └─value[[3L]](cond)
14. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:522:3'): sim_gs_n() can combine wlr(), rmst(), and milestone() tests ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:522:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:620:3'): create_cut() can accept variables as arguments ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:620:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:667:3'): Updating bounds changes the simulation results ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:667:3
2. └─gsDesign2::gs_design_ahr(analysis_time = 1:3 * 12)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:724:3'): sim_gs_n() can update bounds even when some are missing ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:724:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:29:3'): summary.simtrial_gs_wlr() returns consistent results for one-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:29:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:119:3'): summary.simtrial_gs_wlr() returns consistent results for two-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:119:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:3:3'): wlr() accepts tte_data and counting_process objects as input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:3:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:35:3'): wlr() accepts unclassed input object with proper columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:35:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:49:3'): wlr() uses argument ratio ────────────
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(x, weight = fh(rho = 0, gamma = 0.5), ratio = 2) at test-unvalidated-wlr.R:49:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:55:3'): cut_data_by_date() and cut_data_by_event() return the same classes ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 300) at test-unvalidated-wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:63:3'): wlr() formula argument can rename columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:63:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:87:3'): wlr() accepts formula for unstratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:87:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:119:3'): wlr() accepts formula for stratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:119:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:136:3'): wlr() warns when formula argument is ignored ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:136:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:150:3'): wlr.default() and wlr.tte_data() require arm='experimental' ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:150:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘arbitrary-hazard.Rmd’ using rmarkdown
Quitting from arbitrary-hazard.Rmd:68-91 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'arbitrary-hazard.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘arbitrary-hazard.Rmd’
--- re-building ‘discrepancy-between-simtrial-and-survival.Rmd’ using rmarkdown
Quitting from discrepancy-between-simtrial-and-survival.Rmd:92-120 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::fixed_design_mb(...)
3. └─gsDesign2::gs_design_wlr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::gs_info_wlr(...)
6. └─gsDesign2::ahr(...)
7. └─gsDesign2::pw_info(...)
8. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
9. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'discrepancy-between-simtrial-and-survival.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘discrepancy-between-simtrial-and-survival.Rmd’
--- re-building ‘maxcombo.Rmd’ using rmarkdown
Quitting from maxcombo.Rmd:57-69 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...)
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'maxcombo.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘maxcombo.Rmd’
--- re-building ‘modest-wlrt.Rmd’ using rmarkdown
Quitting from modest-wlrt.Rmd:64-79 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'modest-wlrt.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘modest-wlrt.Rmd’
--- re-building ‘parallel.Rmd’ using rmarkdown
Quitting from parallel.Rmd:97-122 [confirm-sequential]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...)
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'parallel.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘parallel.Rmd’
--- re-building ‘rmst.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘rmst.Rmd’
--- re-building ‘routines.Rmd’ using rmarkdown
Quitting from routines.Rmd:135-148 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'routines.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘routines.Rmd’
--- re-building ‘sim_fixed_design_custom.Rmd’ using rmarkdown
Quitting from sim_fixed_design_custom.Rmd:48-63 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─simtrial::sim_pw_surv(...)
2. │ └─base::unique(c(block, fail_rate$treatment, dropout_rate$treatment))
3. └─simtrial::to_sim_pw_surv(fail_rate)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_fixed_design_custom.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘sim_fixed_design_custom.Rmd’
--- re-building ‘sim_fixed_design_simple.Rmd’ using rmarkdown
Quitting from sim_fixed_design_simple.Rmd:58-66 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::fixed_design_ahr(...)
3. └─gsDesign2::gs_design_ahr(...)
4. └─gsDesign2::gs_info_ahr(...)
5. ├─dplyr::select(...)
6. └─gsDesign2::ahr(...)
7. └─gsDesign2::pw_info(...)
8. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
9. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_fixed_design_simple.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘sim_fixed_design_simple.Rmd’
--- re-building ‘sim_gs_design_simple.Rmd’ using rmarkdown
Quitting from sim_gs_design_simple.Rmd:40-62 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_gs_design_simple.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘sim_gs_design_simple.Rmd’
--- re-building ‘workflow.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘workflow.Rmd’
SUMMARY: processing the following files failed:
‘arbitrary-hazard.Rmd’
‘discrepancy-between-simtrial-and-survival.Rmd’ ‘maxcombo.Rmd’
‘modest-wlrt.Rmd’ ‘parallel.Rmd’ ‘routines.Rmd’
‘sim_fixed_design_custom.Rmd’ ‘sim_fixed_design_simple.Rmd’
‘sim_gs_design_simple.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [80s/155s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simtrial)
>
> test_check("simtrial")
Saving _problems/test-developer-get_analysis_date-18.R
Saving _problems/test-developer-get_analysis_date-61.R
Saving _problems/test-double_programming_mb_weight-21.R
Saving _problems/test-double_programming_mb_weight-52.R
Saving _problems/test-double_programming_mb_weight-83.R
Saving _problems/test-double_programming_sim_fixed_n-44.R
Saving _problems/test-double_programming_sim_pw_surv-5.R
Saving _problems/test-double_programming_sim_pw_surv-19.R
Saving _problems/test-double_programming_sim_pw_surv-28.R
Saving _problems/test-double_programming_sim_pw_surv-36.R
Saving _problems/test-double_programming_sim_pw_surv-49.R
Saving _problems/test-double_programming_sim_pw_surv-64.R
Saving _problems/test-independent_test_counting_process-12.R
Saving _problems/test-independent_test_counting_process-32.R
Saving _problems/test-independent_test_cut_data_by_date-2.R
Saving _problems/test-independent_test_cut_data_by_date-16.R
Saving _problems/test-independent_test_cut_data_by_date-27.R
Saving _problems/test-independent_test_cut_data_by_date-37.R
Saving _problems/test-independent_test_cut_data_by_event-2.R
Saving _problems/test-independent_test_early_zero_weight-8.R
Saving _problems/test-independent_test_early_zero_weight-41.R
Saving _problems/test-independent_test_early_zero_weight-95.R
Saving _problems/test-independent_test_early_zero_weight-148.R
Saving _problems/test-independent_test_fh_weight-5.R
Saving _problems/test-independent_test_fh_weight-36.R
Saving _problems/test-independent_test_get_cut_date_by_event-5.R
Saving _problems/test-independent_test_pvalue_maxcombo-7.R
Saving _problems/test-independent_test_simfix2simpwsurv-2.R
Saving _problems/test-independent_test_simfix2simpwsurv-21.R
Saving _problems/test-independent_test_simfix2simpwsurv-35.R
Saving _problems/test-independent_test_simfix2simpwsurv-45.R
Saving _problems/test-independent_test_simfix2simpwsurv-54.R
Saving _problems/test-independent_test_simfix2simpwsurv-64.R
Saving _problems/test-independent_test_simfix2simpwsurv-75.R
Saving _problems/test-independent_test_simfix2simpwsurv-83.R
Saving _problems/test-independent_test_simfix2simpwsurv-91.R
Saving _problems/test-independent_test_simfix2simpwsurv-98.R
Saving _problems/test-independent_test_wlr-7.R
Saving _problems/test-independent_test_wlr-55.R
Saving _problems/test-independent_test_wlr-90.R
Saving _problems/test-independent_test_wlr-144.R
Saving _problems/test-independent_test_wlr-186.R
Saving _problems/test-independent_test_wlr-233.R
Saving _problems/test-unvalidated-data.table-11.R
Saving _problems/test-unvalidated-data.table-70.R
Saving _problems/test-unvalidated-early_zero_weight-8.R
Saving _problems/test-unvalidated-early_zero_weight-43.R
Saving _problems/test-unvalidated-early_zero_weight-92.R
Saving _problems/test-unvalidated-get_analysis_date-4.R
Saving _problems/test-unvalidated-get_analysis_date-12.R
Saving _problems/test-unvalidated-get_analysis_date-20.R
Saving _problems/test-unvalidated-get_analysis_date-32.R
Saving _problems/test-unvalidated-get_analysis_date-43.R
Saving _problems/test-unvalidated-get_analysis_date-55.R
Saving _problems/test-unvalidated-get_analysis_date-67.R
Saving _problems/test-unvalidated-get_analysis_date-81.R
Saving _problems/test-unvalidated-get_analysis_date-93.R
Saving _problems/test-unvalidated-get_analysis_date-105.R
Saving _problems/test-unvalidated-get_analysis_date-120.R
Saving _problems/test-unvalidated-maxcombo-8.R
Saving _problems/test-unvalidated-maxcombo-14.R
Saving _problems/test-unvalidated-multitest-2.R
Backend uses sequential processing.
Saving _problems/test-unvalidated-sim_gs_n-84.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-125.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-166.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-206.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-246.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-285.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-324.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-365.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-413.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-455.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-513.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-529.R
Saving _problems/test-unvalidated-sim_gs_n-625.R
Saving _problems/test-unvalidated-sim_gs_n-668.R
Saving _problems/test-unvalidated-sim_gs_n-734.R
Saving _problems/test-unvalidated-summary-36.R
Saving _problems/test-unvalidated-summary-126.R
Saving _problems/test-unvalidated-wlr-3.R
Saving _problems/test-unvalidated-wlr-35.R
Saving _problems/test-unvalidated-wlr-49.R
Saving _problems/test-unvalidated-wlr-55.R
Saving _problems/test-unvalidated-wlr-63.R
Saving _problems/test-unvalidated-wlr-91.R
Saving _problems/test-unvalidated-wlr-123.R
Saving _problems/test-unvalidated-wlr-136.R
Saving _problems/test-unvalidated-wlr-150.R
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-developer-get_analysis_date.R:2:3'): Cut by targeted event per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-developer-get_analysis_date.R:45:3'): Cut by targeted sample size per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:45:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:19:3'): mb_weight works for single stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:19:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(n = 200)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:32:3'): mb_weight works for multiple strata ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:32:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:63:3'): mb_weight works for a stratum with no records before delay ends ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:63:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_fixed_n.R:24:3'): Double programming of sim_fixed_n ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...) at test-double_programming_sim_fixed_n.R:24:3
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:5:3'): stratum percentage calculated from simulated dataset must be within
the tolerance=0.002 of stratum in setup (0.4,0.6) ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:5:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:19:3'): block calculated from simulated dataset equals size of 4 with 1:1
randomization, which is 2 for each arm ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:19:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:28:3'): fail_rate calculated from simulated dataset must be within the
tolerance=0.1 of fail_rate in setting ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:28:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:36:3'): dropout_rate calculated from simulated dataset must be within
the tolerance=0.0005 of dropout_rate=0.001 in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:36:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:49:3'): enroll_rate calculated from simulated dataset must be within
the relative tolerance=0.05 of enroll_rate in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:49:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:64:3'): The actual number of events changes by changing total sample size ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:64:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:90:3'): sim_pw_surv() fails early with mismatched treatment names ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-double_programming_sim_pw_surv.R:90:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simtrial::sim_pw_surv(block = block, fail_rate = fail_rate, dropout_rate = dropout_rate)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:12:3'): Counting Process Format without ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:12:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:32:3'): Counting Process Format with ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:32:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:2:3'): x is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:16:3'): only patients recorded by cut_data_by_date are included ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:16:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:27:3'): Time-to-event (TTE) is cut off at the cut_date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:27:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:37:3'): the event variable is calculated correctly ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:37:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_event.R:2:3'): the input is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_event.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-independent_test_early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:41:3'): early_zero_weight() with stratified data when fail_rate is not provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:41:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:95:3'): early_zero_weight() with stratified data when fail_rate is not correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:95:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:148:3'): early_zero_weight() with stratified data when fail_rate is correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:148:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:5:3'): the z values match with the correspondings in fh_weight ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:5:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:36:3'): fh_weight calculated correct correlation value when input a sequence of rho and gamma ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:36:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_get_cut_date_by_event.R:5:3'): get_cut_date_by_event returns the correct cut date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_get_cut_date_by_event.R:5:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_pvalue_maxcombo.R:7:3'): the p-values correspond to pvalue_maxcombo ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_pvalue_maxcombo.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:2:3'): stratum values must be the same and stratum length must be doubled after converting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:2:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:21:3'): treatment after converting contains only control and experimental with the right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:21:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:35:3'): Duration values match before and after converting and in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:35:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:45:3'): fail_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:45:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:54:3'): dropout_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:54:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:64:3'): fail_rate column names must contain stratum, duration, fail_rate, hr and dropout_rate ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:64:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:75:3'): duration must be longer than 0 ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:75:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:83:3'): fail_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:83:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:91:3'): hr must be postiive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:91:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:98:3'): dropout_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:98:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:7:3'): wlr() with FH weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:55:3'): wlr() with FH weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:90:3'): wlr() with MB weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:90:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:144:3'): wlr() with MB weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:144:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:186:3'): wlr() with early_zero_weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:186:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:233:3'): wlr() with early_zero_weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:233:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:11:3'): functions that use data.table still return a data frame ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-unvalidated-data.table.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simtrial::counting_process(x, arm = 1)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:70:3'): functions that use data.table do not modify input data table ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm = 1) at test-unvalidated-data.table.R:70:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-unvalidated-early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:43:3'): early_zero_weight() with stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:43:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:92:3'): early_zero_weight() fails with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:92:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:4:3'): planned_calendar_time ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:4:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:12:3'): target_event_overall ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:12:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:20:3'): planned_calendar_time + target_event_overall ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:20:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:32:3'): target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:32:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:43:3'): target_event_overall + target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:43:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:55:3'): target_event_per_stratum + max_extension_for_target_event ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:55:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:67:3'): min_n_overall + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:67:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:81:3'): min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:81:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:93:3'): min_n_per_stratum + min_followup (requirement for only one stratum) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:93:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:105:3'): min_n_overall + min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:105:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:120:3'): get_analysis_date() fails early with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:120:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:6:3'): maxcombo returns consistent results ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::maxcombo(...) at test-unvalidated-maxcombo.R:6:3
2. │ └─simtrial::counting_process(data, arm = "experimental")
3. │ └─base::unique(x$treatment)
4. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150)
5. │ └─simtrial::get_cut_date_by_event(x, event)
6. │ └─data.table::as.data.table(x)
7. └─simtrial::sim_pw_surv(n = 200)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:14:3'): maxcombo fails early with bad input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150) at test-unvalidated-maxcombo.R:14:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-multitest.R:2:3'): multitest() is equivalent to running tests individually ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-unvalidated-multitest.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:75:3'): regular logrank test ────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:75:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:116:3'): regular logrank test parallel ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:116:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:157:3'): weighted logrank test by FH(0, 0.5) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:157:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:197:3'): weighted logrank test by MB(3) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:197:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:237:3'): weighted logrank test by early zero (6) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:237:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:277:3'): RMST ───────────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:277:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:315:3'): Milestone ──────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:315:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:358:3'): WLR with fh(0, 0.5) test at IA1, WLR with mb(6, Inf) at IA2, and milestone test at FA ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:358:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:404:3'): MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5)) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:404:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:448:3'): sim_gs_n() accepts different tests per cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:448:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:503:3'): sim_gs_n() requires a test for each cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-unvalidated-sim_gs_n.R:503:3
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. └─simtrial::sim_gs_n(...)
8. └─... %dofuture% ...
9. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(...)
13. └─value[[3L]](cond)
14. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:522:3'): sim_gs_n() can combine wlr(), rmst(), and milestone() tests ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:522:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:620:3'): create_cut() can accept variables as arguments ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:620:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:667:3'): Updating bounds changes the simulation results ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:667:3
2. └─gsDesign2::gs_design_ahr(analysis_time = 1:3 * 12)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:724:3'): sim_gs_n() can update bounds even when some are missing ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:724:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:29:3'): summary.simtrial_gs_wlr() returns consistent results for one-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:29:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:119:3'): summary.simtrial_gs_wlr() returns consistent results for two-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:119:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:3:3'): wlr() accepts tte_data and counting_process objects as input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:3:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:35:3'): wlr() accepts unclassed input object with proper columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:35:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:49:3'): wlr() uses argument ratio ────────────
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(x, weight = fh(rho = 0, gamma = 0.5), ratio = 2) at test-unvalidated-wlr.R:49:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:55:3'): cut_data_by_date() and cut_data_by_event() return the same classes ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 300) at test-unvalidated-wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:63:3'): wlr() formula argument can rename columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:63:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:87:3'): wlr() accepts formula for unstratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:87:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:119:3'): wlr() accepts formula for stratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:119:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:136:3'): wlr() warns when formula argument is ignored ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:136:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:150:3'): wlr.default() and wlr.tte_data() require arm='experimental' ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:150:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘simtrial-Ex.R’ failed
The error most likely occurred in:
> ### Name: as_gt
> ### Title: Convert summary table to a gt object
> ### Aliases: as_gt as_gt.simtrial_gs_wlr
>
> ### ** Examples
>
>
> # Parameters for enrollment
> enroll_rampup_duration <- 4 # Duration for enrollment ramp up
> enroll_duration <- 16 # Total enrollment duration
> enroll_rate <- gsDesign2::define_enroll_rate(
+ duration = c(
+ enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
+ rate = c(10, 30))
>
> # Parameters for treatment effect
> delay_effect_duration <- 3 # Delay treatment effect in months
> median_ctrl <- 9 # Survival median of the control arm
> median_exp <- c(9, 14) # Survival median of the experimental arm
> dropout_rate <- 0.001
> fail_rate <- gsDesign2::define_fail_rate(
+ duration = c(delay_effect_duration, 100),
+ fail_rate = log(2) / median_ctrl,
+ hr = median_ctrl / median_exp,
+ dropout_rate = dropout_rate)
>
> # Other related parameters
> alpha <- 0.025 # Type I error
> beta <- 0.1 # Type II error
> ratio <- 1 # Randomization ratio (experimental:control)
>
> # Build a one-sided group sequential design
> design <- gsDesign2::gs_design_ahr(
+ enroll_rate = enroll_rate, fail_rate = fail_rate,
+ ratio = ratio, alpha = alpha, beta = beta,
+ analysis_time = c(12, 24, 36),
+ upper = gsDesign2::gs_spending_bound,
+ upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
+ lower = gsDesign2::gs_b,
+ lpar = rep(-Inf, 3))
Error in `[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time)) :
attempt access index 6/6 in VECTOR_ELT
Calls: <Anonymous> ... gs_info_ahr -> select -> ahr -> pw_info -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [4m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simtrial)
>
> test_check("simtrial")
Saving _problems/test-developer-get_analysis_date-18.R
Saving _problems/test-developer-get_analysis_date-61.R
Saving _problems/test-double_programming_mb_weight-21.R
Saving _problems/test-double_programming_mb_weight-52.R
Saving _problems/test-double_programming_mb_weight-83.R
Saving _problems/test-double_programming_sim_fixed_n-44.R
Saving _problems/test-double_programming_sim_pw_surv-5.R
Saving _problems/test-double_programming_sim_pw_surv-19.R
Saving _problems/test-double_programming_sim_pw_surv-28.R
Saving _problems/test-double_programming_sim_pw_surv-36.R
Saving _problems/test-double_programming_sim_pw_surv-49.R
Saving _problems/test-double_programming_sim_pw_surv-64.R
Saving _problems/test-independent_test_counting_process-12.R
Saving _problems/test-independent_test_counting_process-32.R
Saving _problems/test-independent_test_cut_data_by_date-2.R
Saving _problems/test-independent_test_cut_data_by_date-16.R
Saving _problems/test-independent_test_cut_data_by_date-27.R
Saving _problems/test-independent_test_cut_data_by_date-37.R
Saving _problems/test-independent_test_cut_data_by_event-2.R
Saving _problems/test-independent_test_early_zero_weight-8.R
Saving _problems/test-independent_test_early_zero_weight-41.R
Saving _problems/test-independent_test_early_zero_weight-95.R
Saving _problems/test-independent_test_early_zero_weight-148.R
Saving _problems/test-independent_test_fh_weight-5.R
Saving _problems/test-independent_test_fh_weight-36.R
Saving _problems/test-independent_test_get_cut_date_by_event-5.R
Saving _problems/test-independent_test_pvalue_maxcombo-7.R
Saving _problems/test-independent_test_simfix2simpwsurv-2.R
Saving _problems/test-independent_test_simfix2simpwsurv-21.R
Saving _problems/test-independent_test_simfix2simpwsurv-35.R
Saving _problems/test-independent_test_simfix2simpwsurv-45.R
Saving _problems/test-independent_test_simfix2simpwsurv-54.R
Saving _problems/test-independent_test_simfix2simpwsurv-64.R
Saving _problems/test-independent_test_simfix2simpwsurv-75.R
Saving _problems/test-independent_test_simfix2simpwsurv-83.R
Saving _problems/test-independent_test_simfix2simpwsurv-91.R
Saving _problems/test-independent_test_simfix2simpwsurv-98.R
Saving _problems/test-independent_test_wlr-7.R
Saving _problems/test-independent_test_wlr-55.R
Saving _problems/test-independent_test_wlr-90.R
Saving _problems/test-independent_test_wlr-144.R
Saving _problems/test-independent_test_wlr-186.R
Saving _problems/test-independent_test_wlr-233.R
Saving _problems/test-unvalidated-data.table-11.R
Saving _problems/test-unvalidated-data.table-70.R
Saving _problems/test-unvalidated-early_zero_weight-8.R
Saving _problems/test-unvalidated-early_zero_weight-43.R
Saving _problems/test-unvalidated-early_zero_weight-92.R
Saving _problems/test-unvalidated-get_analysis_date-4.R
Saving _problems/test-unvalidated-get_analysis_date-12.R
Saving _problems/test-unvalidated-get_analysis_date-20.R
Saving _problems/test-unvalidated-get_analysis_date-32.R
Saving _problems/test-unvalidated-get_analysis_date-43.R
Saving _problems/test-unvalidated-get_analysis_date-55.R
Saving _problems/test-unvalidated-get_analysis_date-67.R
Saving _problems/test-unvalidated-get_analysis_date-81.R
Saving _problems/test-unvalidated-get_analysis_date-93.R
Saving _problems/test-unvalidated-get_analysis_date-105.R
Saving _problems/test-unvalidated-get_analysis_date-120.R
Saving _problems/test-unvalidated-maxcombo-8.R
Saving _problems/test-unvalidated-maxcombo-14.R
Saving _problems/test-unvalidated-multitest-2.R
Backend uses sequential processing.
Saving _problems/test-unvalidated-sim_gs_n-84.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-125.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-166.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-206.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-246.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-285.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-324.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-365.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-413.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-455.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-513.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-529.R
Saving _problems/test-unvalidated-sim_gs_n-625.R
Saving _problems/test-unvalidated-sim_gs_n-668.R
Saving _problems/test-unvalidated-sim_gs_n-734.R
Saving _problems/test-unvalidated-summary-36.R
Saving _problems/test-unvalidated-summary-126.R
Saving _problems/test-unvalidated-wlr-3.R
Saving _problems/test-unvalidated-wlr-35.R
Saving _problems/test-unvalidated-wlr-49.R
Saving _problems/test-unvalidated-wlr-55.R
Saving _problems/test-unvalidated-wlr-63.R
Saving _problems/test-unvalidated-wlr-91.R
Saving _problems/test-unvalidated-wlr-123.R
Saving _problems/test-unvalidated-wlr-136.R
Saving _problems/test-unvalidated-wlr-150.R
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-developer-get_analysis_date.R:2:3'): Cut by targeted event per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-developer-get_analysis_date.R:45:3'): Cut by targeted sample size per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:45:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:19:3'): mb_weight works for single stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:19:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(n = 200)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:32:3'): mb_weight works for multiple strata ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:32:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:63:3'): mb_weight works for a stratum with no records before delay ends ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:63:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_fixed_n.R:24:3'): Double programming of sim_fixed_n ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...) at test-double_programming_sim_fixed_n.R:24:3
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:5:3'): stratum percentage calculated from simulated dataset must be within
the tolerance=0.002 of stratum in setup (0.4,0.6) ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:5:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:19:3'): block calculated from simulated dataset equals size of 4 with 1:1
randomization, which is 2 for each arm ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:19:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:28:3'): fail_rate calculated from simulated dataset must be within the
tolerance=0.1 of fail_rate in setting ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:28:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:36:3'): dropout_rate calculated from simulated dataset must be within
the tolerance=0.0005 of dropout_rate=0.001 in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:36:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:49:3'): enroll_rate calculated from simulated dataset must be within
the relative tolerance=0.05 of enroll_rate in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:49:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:64:3'): The actual number of events changes by changing total sample size ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:64:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:90:3'): sim_pw_surv() fails early with mismatched treatment names ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-double_programming_sim_pw_surv.R:90:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simtrial::sim_pw_surv(block = block, fail_rate = fail_rate, dropout_rate = dropout_rate)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:12:3'): Counting Process Format without ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:12:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:32:3'): Counting Process Format with ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:32:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:2:3'): x is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:16:3'): only patients recorded by cut_data_by_date are included ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:16:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:27:3'): Time-to-event (TTE) is cut off at the cut_date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:27:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:37:3'): the event variable is calculated correctly ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:37:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_event.R:2:3'): the input is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_event.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-independent_test_early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:41:3'): early_zero_weight() with stratified data when fail_rate is not provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:41:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:95:3'): early_zero_weight() with stratified data when fail_rate is not correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:95:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:148:3'): early_zero_weight() with stratified data when fail_rate is correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:148:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:5:3'): the z values match with the correspondings in fh_weight ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:5:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:36:3'): fh_weight calculated correct correlation value when input a sequence of rho and gamma ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:36:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_get_cut_date_by_event.R:5:3'): get_cut_date_by_event returns the correct cut date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_get_cut_date_by_event.R:5:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_pvalue_maxcombo.R:7:3'): the p-values correspond to pvalue_maxcombo ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_pvalue_maxcombo.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:2:3'): stratum values must be the same and stratum length must be doubled after converting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:2:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:21:3'): treatment after converting contains only control and experimental with the right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:21:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:35:3'): Duration values match before and after converting and in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:35:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:45:3'): fail_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:45:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:54:3'): dropout_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:54:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:64:3'): fail_rate column names must contain stratum, duration, fail_rate, hr and dropout_rate ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:64:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:75:3'): duration must be longer than 0 ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:75:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:83:3'): fail_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:83:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:91:3'): hr must be postiive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:91:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:98:3'): dropout_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:98:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:7:3'): wlr() with FH weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:55:3'): wlr() with FH weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:90:3'): wlr() with MB weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:90:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:144:3'): wlr() with MB weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:144:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:186:3'): wlr() with early_zero_weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:186:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:233:3'): wlr() with early_zero_weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:233:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:11:3'): functions that use data.table still return a data frame ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-unvalidated-data.table.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simtrial::counting_process(x, arm = 1)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:70:3'): functions that use data.table do not modify input data table ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm = 1) at test-unvalidated-data.table.R:70:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-unvalidated-early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:43:3'): early_zero_weight() with stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:43:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:92:3'): early_zero_weight() fails with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:92:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:4:3'): planned_calendar_time ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:4:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:12:3'): target_event_overall ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:12:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:20:3'): planned_calendar_time + target_event_overall ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:20:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:32:3'): target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:32:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:43:3'): target_event_overall + target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:43:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:55:3'): target_event_per_stratum + max_extension_for_target_event ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:55:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:67:3'): min_n_overall + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:67:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:81:3'): min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:81:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:93:3'): min_n_per_stratum + min_followup (requirement for only one stratum) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:93:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:105:3'): min_n_overall + min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:105:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:120:3'): get_analysis_date() fails early with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:120:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:6:3'): maxcombo returns consistent results ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::maxcombo(...) at test-unvalidated-maxcombo.R:6:3
2. │ └─simtrial::counting_process(data, arm = "experimental")
3. │ └─base::unique(x$treatment)
4. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150)
5. │ └─simtrial::get_cut_date_by_event(x, event)
6. │ └─data.table::as.data.table(x)
7. └─simtrial::sim_pw_surv(n = 200)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:14:3'): maxcombo fails early with bad input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150) at test-unvalidated-maxcombo.R:14:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-multitest.R:2:3'): multitest() is equivalent to running tests individually ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-unvalidated-multitest.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:75:3'): regular logrank test ────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:75:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:116:3'): regular logrank test parallel ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:116:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:157:3'): weighted logrank test by FH(0, 0.5) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:157:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:197:3'): weighted logrank test by MB(3) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:197:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:237:3'): weighted logrank test by early zero (6) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:237:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:277:3'): RMST ───────────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:277:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:315:3'): Milestone ──────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:315:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:358:3'): WLR with fh(0, 0.5) test at IA1, WLR with mb(6, Inf) at IA2, and milestone test at FA ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:358:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:404:3'): MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5)) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:404:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:448:3'): sim_gs_n() accepts different tests per cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:448:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:503:3'): sim_gs_n() requires a test for each cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-unvalidated-sim_gs_n.R:503:3
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. └─simtrial::sim_gs_n(...)
8. └─... %dofuture% ...
9. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(...)
13. └─value[[3L]](cond)
14. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:522:3'): sim_gs_n() can combine wlr(), rmst(), and milestone() tests ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:522:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:620:3'): create_cut() can accept variables as arguments ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:620:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:667:3'): Updating bounds changes the simulation results ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:667:3
2. └─gsDesign2::gs_design_ahr(analysis_time = 1:3 * 12)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:724:3'): sim_gs_n() can update bounds even when some are missing ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:724:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:29:3'): summary.simtrial_gs_wlr() returns consistent results for one-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:29:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:119:3'): summary.simtrial_gs_wlr() returns consistent results for two-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:119:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:3:3'): wlr() accepts tte_data and counting_process objects as input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:3:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:35:3'): wlr() accepts unclassed input object with proper columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:35:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:49:3'): wlr() uses argument ratio ────────────
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(x, weight = fh(rho = 0, gamma = 0.5), ratio = 2) at test-unvalidated-wlr.R:49:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:55:3'): cut_data_by_date() and cut_data_by_event() return the same classes ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 300) at test-unvalidated-wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:63:3'): wlr() formula argument can rename columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:63:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:87:3'): wlr() accepts formula for unstratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:87:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:119:3'): wlr() accepts formula for stratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:119:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:136:3'): wlr() warns when formula argument is ignored ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:136:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:150:3'): wlr.default() and wlr.tte_data() require arm='experimental' ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:150:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘arbitrary-hazard.Rmd’ using rmarkdown
Quitting from arbitrary-hazard.Rmd:68-91 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'arbitrary-hazard.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘arbitrary-hazard.Rmd’
--- re-building ‘discrepancy-between-simtrial-and-survival.Rmd’ using rmarkdown
Quitting from discrepancy-between-simtrial-and-survival.Rmd:92-120 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::fixed_design_mb(...)
3. └─gsDesign2::gs_design_wlr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::gs_info_wlr(...)
6. └─gsDesign2::ahr(...)
7. └─gsDesign2::pw_info(...)
8. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
9. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'discrepancy-between-simtrial-and-survival.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘discrepancy-between-simtrial-and-survival.Rmd’
--- re-building ‘maxcombo.Rmd’ using rmarkdown
Quitting from maxcombo.Rmd:57-69 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...)
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'maxcombo.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘maxcombo.Rmd’
--- re-building ‘modest-wlrt.Rmd’ using rmarkdown
Quitting from modest-wlrt.Rmd:64-79 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'modest-wlrt.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘modest-wlrt.Rmd’
--- re-building ‘parallel.Rmd’ using rmarkdown
Quitting from parallel.Rmd:97-122 [confirm-sequential]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...)
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'parallel.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘parallel.Rmd’
--- re-building ‘rmst.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘rmst.Rmd’
--- re-building ‘routines.Rmd’ using rmarkdown
Quitting from routines.Rmd:135-148 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'routines.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘routines.Rmd’
--- re-building ‘sim_fixed_design_custom.Rmd’ using rmarkdown
Quitting from sim_fixed_design_custom.Rmd:48-63 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─simtrial::sim_pw_surv(...)
2. │ └─base::unique(c(block, fail_rate$treatment, dropout_rate$treatment))
3. └─simtrial::to_sim_pw_surv(fail_rate)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_fixed_design_custom.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘sim_fixed_design_custom.Rmd’
--- re-building ‘sim_fixed_design_simple.Rmd’ using rmarkdown
Quitting from sim_fixed_design_simple.Rmd:58-66 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::fixed_design_ahr(...)
3. └─gsDesign2::gs_design_ahr(...)
4. └─gsDesign2::gs_info_ahr(...)
5. ├─dplyr::select(...)
6. └─gsDesign2::ahr(...)
7. └─gsDesign2::pw_info(...)
8. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
9. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_fixed_design_simple.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘sim_fixed_design_simple.Rmd’
--- re-building ‘sim_gs_design_simple.Rmd’ using rmarkdown
Quitting from sim_gs_design_simple.Rmd:40-62 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
▆
1. ├─gsDesign2::to_integer(...)
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sim_gs_design_simple.Rmd' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘sim_gs_design_simple.Rmd’
--- re-building ‘workflow.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘workflow.Rmd’
SUMMARY: processing the following files failed:
‘arbitrary-hazard.Rmd’
‘discrepancy-between-simtrial-and-survival.Rmd’ ‘maxcombo.Rmd’
‘modest-wlrt.Rmd’ ‘parallel.Rmd’ ‘routines.Rmd’
‘sim_fixed_design_custom.Rmd’ ‘sim_fixed_design_simple.Rmd’
‘sim_gs_design_simple.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [221s/391s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(simtrial)
>
> test_check("simtrial")
Saving _problems/test-developer-get_analysis_date-18.R
Saving _problems/test-developer-get_analysis_date-61.R
Saving _problems/test-double_programming_mb_weight-21.R
Saving _problems/test-double_programming_mb_weight-52.R
Saving _problems/test-double_programming_mb_weight-83.R
Saving _problems/test-double_programming_sim_fixed_n-44.R
Saving _problems/test-double_programming_sim_pw_surv-5.R
Saving _problems/test-double_programming_sim_pw_surv-19.R
Saving _problems/test-double_programming_sim_pw_surv-28.R
Saving _problems/test-double_programming_sim_pw_surv-36.R
Saving _problems/test-double_programming_sim_pw_surv-49.R
Saving _problems/test-double_programming_sim_pw_surv-64.R
Saving _problems/test-independent_test_counting_process-12.R
Saving _problems/test-independent_test_counting_process-32.R
Saving _problems/test-independent_test_cut_data_by_date-2.R
Saving _problems/test-independent_test_cut_data_by_date-16.R
Saving _problems/test-independent_test_cut_data_by_date-27.R
Saving _problems/test-independent_test_cut_data_by_date-37.R
Saving _problems/test-independent_test_cut_data_by_event-2.R
Saving _problems/test-independent_test_early_zero_weight-8.R
Saving _problems/test-independent_test_early_zero_weight-41.R
Saving _problems/test-independent_test_early_zero_weight-95.R
Saving _problems/test-independent_test_early_zero_weight-148.R
Saving _problems/test-independent_test_fh_weight-5.R
Saving _problems/test-independent_test_fh_weight-36.R
Saving _problems/test-independent_test_get_cut_date_by_event-5.R
Saving _problems/test-independent_test_pvalue_maxcombo-7.R
Saving _problems/test-independent_test_simfix2simpwsurv-2.R
Saving _problems/test-independent_test_simfix2simpwsurv-21.R
Saving _problems/test-independent_test_simfix2simpwsurv-35.R
Saving _problems/test-independent_test_simfix2simpwsurv-45.R
Saving _problems/test-independent_test_simfix2simpwsurv-54.R
Saving _problems/test-independent_test_simfix2simpwsurv-64.R
Saving _problems/test-independent_test_simfix2simpwsurv-75.R
Saving _problems/test-independent_test_simfix2simpwsurv-83.R
Saving _problems/test-independent_test_simfix2simpwsurv-91.R
Saving _problems/test-independent_test_simfix2simpwsurv-98.R
Saving _problems/test-independent_test_wlr-7.R
Saving _problems/test-independent_test_wlr-55.R
Saving _problems/test-independent_test_wlr-90.R
Saving _problems/test-independent_test_wlr-144.R
Saving _problems/test-independent_test_wlr-186.R
Saving _problems/test-independent_test_wlr-233.R
Saving _problems/test-unvalidated-data.table-11.R
Saving _problems/test-unvalidated-data.table-70.R
Saving _problems/test-unvalidated-early_zero_weight-8.R
Saving _problems/test-unvalidated-early_zero_weight-43.R
Saving _problems/test-unvalidated-early_zero_weight-92.R
Saving _problems/test-unvalidated-get_analysis_date-4.R
Saving _problems/test-unvalidated-get_analysis_date-12.R
Saving _problems/test-unvalidated-get_analysis_date-20.R
Saving _problems/test-unvalidated-get_analysis_date-32.R
Saving _problems/test-unvalidated-get_analysis_date-43.R
Saving _problems/test-unvalidated-get_analysis_date-55.R
Saving _problems/test-unvalidated-get_analysis_date-67.R
Saving _problems/test-unvalidated-get_analysis_date-81.R
Saving _problems/test-unvalidated-get_analysis_date-93.R
Saving _problems/test-unvalidated-get_analysis_date-105.R
Saving _problems/test-unvalidated-get_analysis_date-120.R
Saving _problems/test-unvalidated-maxcombo-8.R
Saving _problems/test-unvalidated-maxcombo-14.R
Saving _problems/test-unvalidated-multitest-2.R
Backend uses sequential processing.
Saving _problems/test-unvalidated-sim_gs_n-84.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-125.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-166.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-206.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-246.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-285.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-324.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-365.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-413.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-455.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-513.R
Using 2 cores with backend multisession
Saving _problems/test-unvalidated-sim_gs_n-529.R
Saving _problems/test-unvalidated-sim_gs_n-625.R
Saving _problems/test-unvalidated-sim_gs_n-668.R
Saving _problems/test-unvalidated-sim_gs_n-734.R
Saving _problems/test-unvalidated-summary-36.R
Saving _problems/test-unvalidated-summary-126.R
Saving _problems/test-unvalidated-wlr-3.R
Saving _problems/test-unvalidated-wlr-35.R
Saving _problems/test-unvalidated-wlr-49.R
Saving _problems/test-unvalidated-wlr-55.R
Saving _problems/test-unvalidated-wlr-63.R
Saving _problems/test-unvalidated-wlr-91.R
Saving _problems/test-unvalidated-wlr-123.R
Saving _problems/test-unvalidated-wlr-136.R
Saving _problems/test-unvalidated-wlr-150.R
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-developer-get_analysis_date.R:2:3'): Cut by targeted event per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-developer-get_analysis_date.R:45:3'): Cut by targeted sample size per stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(...) at test-developer-get_analysis_date.R:45:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:19:3'): mb_weight works for single stratum ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:19:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(n = 200)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:32:3'): mb_weight works for multiple strata ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:32:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_mb_weight.R:63:3'): mb_weight works for a stratum with no records before delay ends ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::counting_process(...) at test-double_programming_mb_weight.R:63:3
2. │ └─base::unique(x$treatment)
3. ├─simtrial::cut_data_by_event(...)
4. │ └─simtrial::get_cut_date_by_event(x, event)
5. │ └─data.table::as.data.table(x)
6. └─simtrial::sim_pw_surv(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_fixed_n.R:24:3'): Double programming of sim_fixed_n ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_fixed_n(...) at test-double_programming_sim_fixed_n.R:24:3
2. └─simtrial::to_sim_pw_surv(fail_rate)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:5:3'): stratum percentage calculated from simulated dataset must be within
the tolerance=0.002 of stratum in setup (0.4,0.6) ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:5:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:19:3'): block calculated from simulated dataset equals size of 4 with 1:1
randomization, which is 2 for each arm ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:19:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:28:3'): fail_rate calculated from simulated dataset must be within the
tolerance=0.1 of fail_rate in setting ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:28:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:36:3'): dropout_rate calculated from simulated dataset must be within
the tolerance=0.0005 of dropout_rate=0.001 in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:36:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:49:3'): enroll_rate calculated from simulated dataset must be within
the relative tolerance=0.05 of enroll_rate in setup ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:49:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:64:3'): The actual number of events changes by changing total sample size ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_sim_pw_surv() at test-double_programming_sim_pw_surv.R:64:3
2. └─simtrial::sim_pw_surv(...) at ./helper-sim_pw_surv.R:27:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-double_programming_sim_pw_surv.R:90:3'): sim_pw_surv() fails early with mismatched treatment names ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-double_programming_sim_pw_surv.R:90:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─simtrial::sim_pw_surv(block = block, fail_rate = fail_rate, dropout_rate = dropout_rate)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:12:3'): Counting Process Format without ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:12:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_counting_process.R:32:3'): Counting Process Format with ties ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm) at test-independent_test_counting_process.R:32:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:2:3'): x is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:16:3'): only patients recorded by cut_data_by_date are included ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:16:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:27:3'): Time-to-event (TTE) is cut off at the cut_date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:27:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_date.R:37:3'): the event variable is calculated correctly ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_date.R:37:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_cut_data_by_event.R:2:3'): the input is a time-to-event data set ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_cut_data_by_event.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-independent_test_early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:41:3'): early_zero_weight() with stratified data when fail_rate is not provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:41:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:95:3'): early_zero_weight() with stratified data when fail_rate is not correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:95:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_early_zero_weight.R:148:3'): early_zero_weight() with stratified data when fail_rate is correctly provided ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_early_zero_weight.R:148:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:5:3'): the z values match with the correspondings in fh_weight ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:5:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_fh_weight.R:36:3'): fh_weight calculated correct correlation value when input a sequence of rho and gamma ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_fh_weight.R:36:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_get_cut_date_by_event.R:5:3'): get_cut_date_by_event returns the correct cut date ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-independent_test_get_cut_date_by_event.R:5:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_pvalue_maxcombo.R:7:3'): the p-values correspond to pvalue_maxcombo ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 30) at test-independent_test_pvalue_maxcombo.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:2:3'): stratum values must be the same and stratum length must be doubled after converting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:2:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:21:3'): treatment after converting contains only control and experimental with the right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:21:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:35:3'): Duration values match before and after converting and in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:35:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:45:3'): fail_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:45:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:54:3'): dropout_rate match before and after converting and are in right length ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:54:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:64:3'): fail_rate column names must contain stratum, duration, fail_rate, hr and dropout_rate ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:64:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:75:3'): duration must be longer than 0 ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:75:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:83:3'): fail_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:83:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:91:3'): hr must be postiive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:91:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_simfix2simpwsurv.R:98:3'): dropout_rate must be smaller than 1 and positive ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_simfix2simpwsurv() at test-independent_test_simfix2simpwsurv.R:98:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-simfix2simpwsurv.R:18:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:7:3'): wlr() with FH weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:7:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:55:3'): wlr() with FH weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:90:3'): wlr() with MB weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:90:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:144:3'): wlr() with MB weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:144:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:186:3'): wlr() with early_zero_weight on unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125) at test-independent_test_wlr.R:186:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-independent_test_wlr.R:233:3'): wlr() with early_zero_weight on stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-independent_test_wlr.R:233:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:11:3'): functions that use data.table still return a data frame ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-unvalidated-data.table.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simtrial::counting_process(x, arm = 1)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-data.table.R:70:3'): functions that use data.table do not modify input data table ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::counting_process(x, arm = 1) at test-unvalidated-data.table.R:70:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:5:3'): early_zero_weight() with unstratified data ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial:::early_zero_weight(...) at test-unvalidated-early_zero_weight.R:5:3
2. │ └─data.table::as.data.table(x)
3. ├─simtrial::counting_process(...)
4. │ └─base::unique(x$treatment)
5. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 125)
6. │ └─simtrial::get_cut_date_by_event(x, event)
7. │ └─data.table::as.data.table(x)
8. └─simtrial::sim_pw_surv(n = 200)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:43:3'): early_zero_weight() with stratified data ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:43:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-early_zero_weight.R:92:3'): early_zero_weight() fails with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::to_sim_pw_surv(fail_rate) at test-unvalidated-early_zero_weight.R:92:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:4:3'): planned_calendar_time ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:4:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:12:3'): target_event_overall ───
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:12:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:20:3'): planned_calendar_time + target_event_overall ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:20:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:32:3'): target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:32:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:43:3'): target_event_overall + target_event_per_stratum ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:43:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:55:3'): target_event_per_stratum + max_extension_for_target_event ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:55:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:67:3'): min_n_overall + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:67:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:81:3'): min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:81:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:93:3'): min_n_per_stratum + min_followup (requirement for only one stratum) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:93:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:105:3'): min_n_overall + min_n_per_stratum + min_followup ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:105:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-get_analysis_date.R:120:3'): get_analysis_date() fails early with bad input ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial:::test_get_analysis_date() at test-unvalidated-get_analysis_date.R:120:3
2. └─simtrial::to_sim_pw_surv(fail_rate) at ./helper-get_analysis_date.R:34:3
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:6:3'): maxcombo returns consistent results ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::maxcombo(...) at test-unvalidated-maxcombo.R:6:3
2. │ └─simtrial::counting_process(data, arm = "experimental")
3. │ └─base::unique(x$treatment)
4. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150)
5. │ └─simtrial::get_cut_date_by_event(x, event)
6. │ └─data.table::as.data.table(x)
7. └─simtrial::sim_pw_surv(n = 200)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-maxcombo.R:14:3'): maxcombo fails early with bad input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 200), 150) at test-unvalidated-maxcombo.R:14:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 200)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-multitest.R:2:3'): multitest() is equivalent to running tests individually ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 200) at test-unvalidated-multitest.R:2:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:75:3'): regular logrank test ────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:75:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:116:3'): regular logrank test parallel ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:116:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:157:3'): weighted logrank test by FH(0, 0.5) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:157:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:197:3'): weighted logrank test by MB(3) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:197:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:237:3'): weighted logrank test by early zero (6) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-unvalidated-sim_gs_n.R:237:3
2. └─simtrial::sim_gs_n(...)
3. └─... %dofuture% ...
4. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(...)
8. └─value[[3L]](cond)
9. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:277:3'): RMST ───────────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:277:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:315:3'): Milestone ──────────────────────
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:315:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:358:3'): WLR with fh(0, 0.5) test at IA1, WLR with mb(6, Inf) at IA2, and milestone test at FA ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:358:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:404:3'): MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5)) ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:404:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:448:3'): sim_gs_n() accepts different tests per cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:448:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:503:3'): sim_gs_n() requires a test for each cutting ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-unvalidated-sim_gs_n.R:503:3
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. └─simtrial::sim_gs_n(...)
8. └─... %dofuture% ...
9. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(...)
13. └─value[[3L]](cond)
14. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:522:3'): sim_gs_n() can combine wlr(), rmst(), and milestone() tests ──
Error in ``[.data.table`(fr_control, , `:=`(treatment = "control", rate = fail_rate, period = seq_len(.N)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_gs_n(...) at test-unvalidated-sim_gs_n.R:522:3
2. └─... %dofuture% ...
3. └─doFuture:::doFuture2(foreach, expr, envir = parent.frame(), data = NULL)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(...)
7. └─value[[3L]](cond)
8. └─doFuture:::onError(e, futures = fs, debug = debug)
── Error ('test-unvalidated-sim_gs_n.R:620:3'): create_cut() can accept variables as arguments ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:620:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:667:3'): Updating bounds changes the simulation results ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:667:3
2. └─gsDesign2::gs_design_ahr(analysis_time = 1:3 * 12)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-sim_gs_n.R:724:3'): sim_gs_n() can update bounds even when some are missing ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─gsDesign2::to_integer(...) at test-unvalidated-sim_gs_n.R:724:3
2. └─gsDesign2::gs_design_ahr(...)
3. └─gsDesign2::gs_info_ahr(...)
4. ├─dplyr::select(...)
5. └─gsDesign2::ahr(...)
6. └─gsDesign2::pw_info(...)
7. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
8. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:29:3'): summary.simtrial_gs_wlr() returns consistent results for one-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:29:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-summary.R:119:3'): summary.simtrial_gs_wlr() returns consistent results for two-sided design ──
Error in ``[.data.table`(tbl_event, , `:=`(info0, event * q_c * q_e), by = .(time))`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. └─gsDesign2::gs_design_ahr(...) at test-unvalidated-summary.R:119:3
2. └─gsDesign2::gs_info_ahr(...)
3. ├─dplyr::select(...)
4. └─gsDesign2::ahr(...)
5. └─gsDesign2::pw_info(...)
6. ├─tbl_event[, `:=`(info0, event * q_c * q_e), by = .(time)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:3:3'): wlr() accepts tte_data and counting_process objects as input ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:3:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:35:3'): wlr() accepts unclassed input object with proper columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:35:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:49:3'): wlr() uses argument ratio ────────────
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(x, weight = fh(rho = 0, gamma = 0.5), ratio = 2) at test-unvalidated-wlr.R:49:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:55:3'): cut_data_by_date() and cut_data_by_event() return the same classes ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simtrial::sim_pw_surv(n = 300) at test-unvalidated-wlr.R:55:3
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:63:3'): wlr() formula argument can rename columns ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:63:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:87:3'): wlr() accepts formula for unstratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:87:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:119:3'): wlr() accepts formula for stratified design ──
Error in ``[.data.table`(ans, , `:=`(n_risk_total = cumsum(one), n_risk_trt = cumsum(treatment == arm)), by = "stratum")`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::wlr(...) at test-unvalidated-wlr.R:119:3
2. └─simtrial:::wlr.default(...)
3. └─simtrial:::wlr.tte_data(...)
4. └─simtrial::counting_process(data, arm = "experimental")
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:136:3'): wlr() warns when formula argument is ignored ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:136:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-unvalidated-wlr.R:150:3'): wlr.default() and wlr.tte_data() require arm='experimental' ──
Error in ``[.data.table`(x, , `:=`(treatment, randomize_by_fixed_block(n = .N, block = block)), by = "stratum")`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. ├─simtrial::cut_data_by_event(sim_pw_surv(n = 300), 100) at test-unvalidated-wlr.R:150:3
2. │ └─simtrial::get_cut_date_by_event(x, event)
3. │ └─data.table::as.data.table(x)
4. └─simtrial::sim_pw_surv(n = 300)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 89 | WARN 12 | SKIP 0 | PASS 77 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc