Last updated on 2026-10-24 01:51:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 14.54 | 237.30 | 251.84 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 9.63 | 130.86 | 140.49 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 14.00 | 186.69 | 200.69 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 10.00 | 167.25 | 177.25 | OK | |
| r-devel-windows-x86_64 | 1.1.1 | 17.00 | 267.00 | 284.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 14.27 | 230.21 | 244.48 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 14.70 | 226.91 | 241.61 | OK | |
| r-release-macos-arm64 | 1.1.1 | 4.00 | 64.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 10.00 | 263.00 | 273.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 16.00 | 261.00 | 277.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.1 | 9.00 | 264.00 | 273.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.1 | 22.00 | 337.00 | 359.00 | OK |
Version: 1.1.1
Check: examples
Result: ERROR
Running examples in ‘success-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bk_control_limit
> ### Title: Determine control limits for BK-CUSUM by simulation
> ### Aliases: bk_control_limit
>
> ### ** Examples
>
> require(survival)
Loading required package: survival
>
> #Determine a cox proportional hazards model for risk-adjustment
> exprfit <- as.formula("Surv(survtime, censorid) ~ age + sex + BMI")
> tcoxmod <- coxph(exprfit, data= surgerydat)
>
> #Determine a control limit restricting type I error to 0.1 over 500 days
> #with specified cumulative hazard function without risk-adjustment
> a <- bk_control_limit(time = 500, alpha = 0.1, theta = log(2),
+ cbaseh = function(t) chaz_exp(t, lambda = 0.02),
+ inv_cbaseh = function(t) inv_chaz_exp(t, lambda = 0.02), psi = 0.5,
+ n_sim = 10)
>
> #Determine a control limit restricting type I error to 0.1 over 500 days
> #using the risk-adjusted cumulative hazard determined using coxph()
> b <- bk_control_limit(time = 500, alpha = 0.1, theta = log(2),
+ coxphmod = tcoxmod, psi = 0.5, n_sim = 10)
Error in a$specials[[i]] : subscript out of bounds
Calls: bk_control_limit ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(success)
Loading required package: ggplot2
Loading required package: pbapply
Loading required package: plotly
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Loading required package: Rfast
Loading required package: Rcpp
Loading required package: zigg
Loading required package: RcppParallel
Attaching package: 'RcppParallel'
The following object is masked from 'package:Rcpp':
LdFlags
Rfast: 2.1.5.2
___ __ __ __ __ __ __ __ __ __ _ _ __ __ __ __ __ __ __ __ __ __ __
| __ __ __ __ | | __ __ __ __ _/ / \ | __ __ __ __ / /__ __ _ _ __ __\
| | | | | | / _ \ | | / /
| | | | | | / / \ \ | | / /
| | | | | | / / \ \ | | / /
| |__ __ __ __| | | |__ __ __ __ / / \ \ | |__ __ __ __ _ / /__/\
| __ __ __ __| | __ __ __ __| / /__ _ __\ \ |_ __ __ __ _ | / ___ /
| \ | | / _ _ _ _ _ _ \ | | \/ / /
| |\ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \ | | / / \ \ | | / /
| | \ \__ __ _ | | / / \ \ _ __ __ __ _| | / /
|_| \__ __ __\ |_| /_/ \_\ /_ __ __ __ ___| \/ team
>
> test_check("success")
Step 1/3: Generating in-control data.
Step 2/3: Determining Bernoulli CUSUM chart(s).
Step 3/3: Determining control limits
Loading required package: survival
Saving _problems/test-bk_control_limit-29.R
Saving _problems/test-bk_control_limit-61.R
Saving _problems/test-bk_cusum-30.R
Saving _problems/test-bk_cusum-47.R
Saving _problems/test-bk_cusum-59.R
Saving _problems/test-bk_cusum-70.R
Saving _problems/test-bk_cusum-91.R
Saving _problems/test-calc_risk-23.R
Step 1/3: Generating in-control data.
Saving _problems/test-cgr_control_limit-37.R
Saving _problems/test-cgr_control_limit-57.R
Saving _problems/test-cgr_cusum-40.R
Saving _problems/test-cgr_cusum-51.R
Saving _problems/test-cgr_cusum-64.R
Saving _problems/test-cgr_cusum-73.R
Saving _problems/test-cgr_cusum-87.R
|
| | 0%Saving _problems/test-cgr_generic-30.R
Saving _problems/test-cgr_generic-50.R
Saving _problems/test-runlength-18.R
Saving _problems/test-runlength-63.R
[ FAIL 21 | WARN 0 | SKIP 3 | PASS 123 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-bernoulli_ARL.R:93:1', 'test-bk_control_limit.R:44:3'
• Skipping (1): 'test-cgr_cusum.R:24:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-bk_control_limit.R:28:3'): Output checks ───────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_control_limit(...) at test-bk_control_limit.R:28:3
2. └─success::generate_units(...)
3. └─success::extract_hazard(coxphmod)
4. └─survival::basehaz(coxphmod, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_control_limit.R:60:3'): Theory ──────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_control_limit(...) at test-bk_control_limit.R:60:3
2. └─success::generate_units(...)
3. └─success::extract_hazard(coxphmod)
4. └─survival::basehaz(coxphmod, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_cusum.R:29:3'): output checks ───────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(...) at test-bk_cusum.R:29:3
2. └─success::calc_risk(data = data, coxphmod = coxphmod)
3. ├─stats::predict(...)
4. └─survival:::predict.coxph(...)
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_cusum.R:46:3'): Automatic cbaseh determination ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(data = tdat, theta = log(2), coxphmod = tcoxmod) at test-bk_cusum.R:46:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_cusum.R:58:3'): Lower sided CUSUM ───────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(data = tdat, theta = -log(2), coxphmod = tcoxmod) at test-bk_cusum.R:58:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_cusum.R:69:3'): Two-sided vs one-sided ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(data = tdat, theta = log(2), coxphmod = tcoxmod) at test-bk_cusum.R:69:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-bk_cusum.R:91:3'): parameter assist works as expected ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(assist = pars) at test-bk_cusum.R:91:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-calc_risk.R:23:3'): survival package vs manual RA ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_length(calc_risk(crdat, phmod), nrow(crdat)) at test-calc_risk.R:23:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─success::calc_risk(crdat, phmod)
5. ├─stats::predict(...)
6. └─survival:::predict.coxph(...)
7. └─stats::delete.response(Terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_control_limit.R:19:3'): input checks ───────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-cgr_control_limit.R:19:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─success::cgr_control_limit(...)
11. └─success::generate_units(...)
12. └─success::extract_hazard(coxphmod)
13. └─survival::basehaz(coxphmod, centered = FALSE)
14. ├─survival::survfit(fit, se.fit = FALSE)
15. └─survival:::survfit.coxph(fit, se.fit = FALSE)
16. └─survival:::model.matrix.coxph(object, data = mf)
17. └─stats::delete.response(object$terms)
18. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_control_limit.R:36:3'): Theory ─────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_control_limit(...) at test-cgr_control_limit.R:36:3
2. └─success::generate_units(...)
3. └─success::extract_hazard(coxphmod)
4. └─survival::basehaz(coxphmod, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_control_limit.R:56:3'): Don't risk-adjust when no baseline_data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_control_limit(...) at test-cgr_control_limit.R:56:3
2. └─success::generate_units(...)
3. └─success::extract_hazard(coxphmod)
4. └─survival::basehaz(coxphmod, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_cusum.R:40:3'): Specifying C reduces ctimes ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_cusum(data = tdat, coxphmod = tcoxmod) at test-cgr_cusum.R:40:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_cusum.R:51:3'): maxtheta is working as intended ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_cusum(data = tdat, coxphmod = tcoxmod, cbaseh = tcbaseh) at test-cgr_cusum.R:51:3
2. └─success:::cgr_helper_mat(...)
3. └─success::calc_risk(data, coxphmod)
4. ├─stats::predict(...)
5. └─survival:::predict.coxph(...)
6. └─stats::delete.response(Terms)
7. └─stats (local) off(a$specials[[i]])
── Failure ('test-cgr_cusum.R:64:3'): CPU also works + progress bar ────────────
Expected `cgr_cusum(data = tdat, coxphmod = tcoxmod, cmethod = "CPU")` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-cgr_cusum.R:65:3'): CPU also works + progress bar ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_output(...) at test-cgr_cusum.R:65:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─success::cgr_cusum(...)
11. └─success::extract_hazard(coxphmod)
12. └─survival::basehaz(coxphmod, centered = FALSE)
13. ├─survival::survfit(fit, se.fit = FALSE)
14. └─survival:::survfit.coxph(fit, se.fit = FALSE)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_cusum.R:73:3'): specifying control limit works ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_cusum(data = tdat, coxphmod = tcoxmod, h = 4) at test-cgr_cusum.R:73:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_cusum.R:87:3'): parameter assist works as expected ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_cusum(assist = pars) at test-cgr_cusum.R:87:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_generic.R:30:5'): BK-CUSUM plot ────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(...) at test-cgr_generic.R:30:5
2. └─success::calc_risk(data = data, coxphmod = coxphmod)
3. ├─stats::predict(...)
4. └─survival:::predict.coxph(...)
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-cgr_generic.R:50:5'): CGR-CUSUM plot ───────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::cgr_cusum(...) at test-cgr_generic.R:50:5
2. └─success:::cgr_helper_mat(...)
3. └─success::calc_risk(data, coxphmod)
4. ├─stats::predict(...)
5. └─survival:::predict.coxph(...)
6. └─stats::delete.response(Terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-runlength.R:18:3'): Input checks ───────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(data = tdat, theta = log(2), coxphmod = tcoxmod) at test-runlength.R:18:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-runlength.R:63:3'): Output checks ──────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─success::bk_cusum(data = tdat, theta = log(2), coxphmod = tcoxmod) at test-runlength.R:63:3
2. └─success::extract_hazard(coxphmod)
3. └─survival::basehaz(coxphmod, centered = FALSE)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
[ FAIL 21 | WARN 0 | SKIP 3 | PASS 123 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc