Last updated on 2026-10-24 09:50:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 6.58 | 198.73 | 205.31 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 5.43 | 72.44 | 77.87 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 6.00 | 142.48 | 148.48 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 6.00 | 145.23 | 151.23 | OK | |
| r-devel-windows-x86_64 | 0.1.1 | 9.00 | 190.00 | 199.00 | OK | |
| r-patched-linux-x86_64 | 0.1.1 | 7.73 | 187.83 | 195.56 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 6.12 | 189.92 | 196.04 | OK | |
| r-release-macos-arm64 | 0.1.1 | 2.00 | 42.00 | 44.00 | OK | |
| r-release-macos-x86_64 | 0.1.1 | 5.00 | 267.00 | 272.00 | OK | |
| r-release-windows-x86_64 | 0.1.1 | 11.00 | 179.00 | 190.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 3.00 | 52.00 | 55.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.1 | 5.00 | 200.00 | 205.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.1 | 12.00 | 267.00 | 279.00 | OK |
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘ertte-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ertte_fun
> ### Title: Prediction function for an exposure-response TTE model
> ### Aliases: ertte_fun ertte_fun.ertte_aft ertte_fun.ertte_coxph
>
> ### ** Examples
>
> # fit an AFT model
> mod_aft <- ertte_aft(Surv(time, event) ~ aucss, ertte_data)
> mod_aft_fun <- ertte_fun(mod_aft)
>
> # when called with no arguments it reproduces the fitted
> # model's own survival predictions
> s1 <- mod_aft_fun(time = 60)
> s1[1:5]
[1] 0.3925581 0.5653608 0.7080801 0.7080801 0.2939277
>
> # when called with an explicit parameter vector, the model
> # is evaluated at those modified parameters
> par_new <- coef(mod_aft)
> par_new["(Intercept)"] <- par_new["(Intercept)"] + 1
> s2 <- mod_aft_fun(param = par_new, time = 60)
> s2[1:5]
[1] 0.7933096 0.8683024 0.9180736 0.9180736 0.7384583
>
> # the same logic applies for Cox regression models
> mod_cox <- ertte_coxph(Surv(time, event) ~ aucss, ertte_data)
> mod_cox_fun <- ertte_fun(mod_cox)
Error in a$specials[[i]] : subscript out of bounds
Calls: ertte_fun -> ertte_fun.ertte_coxph -> <Anonymous> -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ertte)
>
> test_check("ertte")
Saving _problems/test-er-methods-65.R
Saving _problems/test-er-methods-132.R
Saving _problems/test-er-methods-146.R
Saving _problems/test-er-methods-295.R
Saving _problems/test-er-methods-311.R
Saving _problems/test-er-methods-453.R
Saving _problems/test-ertte-censoring-31.R
Saving _problems/test-ertte-censoring-71.R
Saving _problems/test-ertte-coxph-69.R
Saving _problems/test-ertte-coxph-77.R
Saving _problems/test-ertte-coxph-89.R
Saving _problems/test-ertte-coxph-99.R
Saving _problems/test-ertte-coxph-105.R
Saving _problems/test-ertte-coxph-116.R
Saving _problems/test-ertte-coxph-139.R
Saving _problems/test-ertte-coxph-152.R
Saving _problems/test-ertte-coxph-159.R
Saving _problems/test-ertte-coxph-185.R
Saving _problems/test-ertte-coxph-199.R
Saving _problems/test-ertte-coxph-206.R
Saving _problems/test-ertte-coxph-228.R
Saving _problems/test-ertte-edge-cases-77.R
Saving _problems/test-ertte-edge-cases-105.R
Saving _problems/test-ertte-edge-cases-117.R
Saving _problems/test-ertte-edge-cases-168.R
Saving _problems/test-ertte-edge-cases-190.R
Saving _problems/test-ertte-landmark-16.R
Saving _problems/test-ertte-landmark-82.R
Saving _problems/test-ertte-power-62.R
Saving _problems/test-ertte-rmst-18.R
Saving _problems/test-ertte-rmst-32.R
Saving _problems/test-ertte-rmst-53.R
Saving _problems/test-ertte-rmst-91.R
Saving _problems/test-ertte-rmst-109.R
Saving _problems/test-ertte-rmst-125.R
Saving _problems/test-ertte-rmst-174.R
[ FAIL 36 | WARN 1 | SKIP 0 | PASS 293 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-er-methods.R:65:3'): er_simulate.ertte_model() with tau adds fit_resp/sim_resp, matching ertte_rmst() ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ertte:::er_simulate.ertte_model(...) at test-er-methods.R:65:3
2. ├─ertte:::.ertte_simulate_draws(...)
3. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
4. └─stats::delete.response(stats::terms(object))
5. └─stats (local) off(a$specials[[i]])
── Error ('test-er-methods.R:129:3'): er_predict_survival.ertte_model() matches ertte_predict() for strictly positive time_grid ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-er-methods.R:129:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ertte:::er_predict_survival.ertte_model(mod_cox, nd, tg)
5. ├─ertte::ertte_predict(...)
6. └─ertte:::ertte_predict.ertte_coxph(...)
7. ├─survival::survfit(...)
8. └─survival:::survfit.coxph(...)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-er-methods.R:146:5'): er_predict_survival.ertte_model() treats time_grid = 0 as S(0) = 1, for both engines ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ertte:::er_predict_survival.ertte_model(mod, nd, tg) at test-er-methods.R:146:5
2. ├─ertte::ertte_predict(...)
3. └─ertte:::ertte_predict.ertte_coxph(...)
4. ├─survival::survfit(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-er-methods.R:295:3'): er_predict_survival.ertte_model() propagates NA for a single-level-factor ertte_aft model, but returns finite values for ertte_coxph ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ertte:::er_predict_survival.ertte_model(...) at test-er-methods.R:295:3
2. ├─ertte::ertte_predict(...)
3. └─ertte:::ertte_predict.ertte_coxph(...)
4. ├─survival::survfit(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-er-methods.R:309:3'): er_tte_add_model() renders one curve per stratum for an ertte_coxph model ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─erplots::er_tte_add_model(...) at test-er-methods.R:309:3
2. └─erplots:::.layer_tte_model(...)
3. └─erplots:::.compute_tte_model_config(object, config)
4. ├─rlang::exec(...)
5. ├─erplots (local) `<fn>`(...)
6. └─ertte:::er_predict_survival.ertte_model(...)
7. ├─ertte::ertte_predict(...)
8. └─ertte:::ertte_predict.ertte_coxph(...)
9. ├─survival::survfit(...)
10. └─survival:::survfit.coxph(...)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test-er-methods.R:448:3'): tau reaches an RMST VPC through erplots' er_vpc_add_simulated(simulate_args = ...) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─erplots::er_vpc_add_simulated(...) at test-er-methods.R:448:3
2. ├─rlang::exec(...)
3. ├─erplots (local) `<fn>`(...)
4. └─ertte:::er_simulate.ertte_model(...)
5. ├─ertte:::.ertte_simulate_draws(...)
6. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
7. └─stats::delete.response(stats::terms(object))
8. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-censoring.R:31:3'): default simulation leaves event rows uncensored (ertte_coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, nsim = 30, seed = 502) at test-ertte-censoring.R:31:3
2. └─ertte:::simulate.ertte_model(mod, nsim = 30, seed = 502)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-censoring.R:71:3'): coxph simulation treats draws beyond the baseline hazard's support as censored, not events ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, nsim = 200, seed = 506) at test-ertte-censoring.R:71:3
2. └─ertte:::simulate.ertte_model(mod, nsim = 200, seed = 506)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:69:3'): ertte_fun() on ertte_coxph reproduces the fitted model's own predictions ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:69:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:77:3'): ertte_fun() on ertte_coxph works with custom newdata and vectorised time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:77:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:89:3'): ertte_fun() on ertte_coxph responds to a custom param ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:89:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:99:3'): ertte_fun() on ertte_coxph checks param length ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:99:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:105:3'): ertte_fun() on ertte_coxph validates time the same way ertte_predict() does ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:105:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:116:3'): ertte_fun() on ertte_coxph's closure takes data before param (issue #6) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_fun(mod) at test-ertte-coxph.R:116:3
2. └─ertte:::ertte_fun.ertte_coxph(mod)
3. └─stats::delete.response(stats::terms(object))
4. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:139:3'): ertte_predict() on ertte_coxph returns a tidy tibble with sane survival probabilities ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(...) at test-ertte-coxph.R:139:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:152:3'): ertte_predict() on ertte_coxph handles a single-row newdata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(...) at test-ertte-coxph.R:152:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:159:3'): ertte_predict() on ertte_coxph extrapolates times beyond the observed range ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(...) at test-ertte-coxph.R:159:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:185:3'): simulate() on ertte_coxph has the expected shape ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, nsim = 5, seed = 321) at test-ertte-coxph.R:185:3
2. └─ertte:::simulate.ertte_model(mod, nsim = 5, seed = 321)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:199:3'): simulate() on ertte_coxph is reproducible given a seed ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, nsim = 5, seed = 42) at test-ertte-coxph.R:199:3
2. └─ertte:::simulate.ertte_model(mod, nsim = 5, seed = 42)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:206:3'): simulate() on ertte_coxph reports an auto-picked seed ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_message(simulate(mod, nsim = 5), "Using seed") at test-ertte-coxph.R:206:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─stats::simulate(mod, nsim = 5)
8. └─ertte:::simulate.ertte_model(mod, nsim = 5)
9. └─ertte:::.ertte_resample(...)
10. ├─ertte:::.ertte_simulate_draws(...)
11. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
12. └─stats::delete.response(stats::terms(object))
13. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-coxph.R:228:3'): simulate() on ertte_coxph reproduces the fitted baseline survival curve ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, nsim = 1, newdata = nd, seed = 777) at test-ertte-coxph.R:228:3
2. └─ertte:::simulate.ertte_model(mod, nsim = 1, newdata = nd, seed = 777)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-edge-cases.R:77:3'): ertte_predict.ertte_coxph() still returns finite predictions for an aliased single-level factor term ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(mod, dat[1:3, ], time = c(30, 60)) at test-ertte-edge-cases.R:77:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-edge-cases.R:105:3'): ertte_coxph() fits normally under heavy ties in event times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(mod, dat[1:5, ], time = c(30, 60)) at test-ertte-edge-cases.R:105:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-edge-cases.R:117:3'): simulate() reproduces sensible event times under heavy ties ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::simulate(mod, newdata = dat[1:10, ], nsim = 5, seed = 33) at test-ertte-edge-cases.R:117:3
2. └─ertte:::simulate.ertte_model(...)
3. └─ertte:::.ertte_resample(...)
4. ├─ertte:::.ertte_simulate_draws(...)
5. └─ertte:::.ertte_simulate_draws.ertte_coxph(...)
6. └─stats::delete.response(stats::terms(object))
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-edge-cases.R:168:3'): ertte_predict.ertte_coxph() handles conf_level = 0/1 like ertte_predict.ertte_aft() does ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(mod_cox, nd3, time = 30, conf_level = 0) at test-ertte-edge-cases.R:168:3
2. └─ertte:::ertte_predict.ertte_coxph(mod_cox, nd3, time = 30, conf_level = 0)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-edge-cases.R:190:3'): ertte_rmst.ertte_coxph() handles conf_level = 0/1 without erroring, matching the AFT engine's pattern ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_rmst(mod_cox, nd3, tau = 60, conf_level = 0) at test-ertte-edge-cases.R:190:3
2. └─ertte:::ertte_rmst.ertte_coxph(mod_cox, nd3, tau = 60, conf_level = 0)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-landmark.R:16:3'): ertte_landmark() is 1 - ertte_predict() with CI bounds swapped (Cox PH) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ertte::ertte_landmark(mod, nd, landmark_time = 90) at test-ertte-landmark.R:16:3
2. ├─ertte::ertte_predict(...)
3. └─ertte:::ertte_predict.ertte_coxph(...)
4. ├─survival::survfit(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-landmark.R:82:5'): ertte_landmark() recomputes landmark_time/fit_resp/ci_lower/ci_upper even when newdata already has columns of those names ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ertte::ertte_landmark(mod, grid, landmark_time = 90) at test-ertte-landmark.R:82:5
2. ├─ertte::ertte_predict(...)
3. └─ertte:::ertte_predict.ertte_coxph(...)
4. ├─survival::survfit(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-power.R:62:3'): ertte_coxph() also reuses the fitting-time ref via survfit() ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_predict(mod, newdata, time = c(30, 60)) at test-ertte-power.R:62:3
2. └─ertte:::ertte_predict.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:18:3'): ertte_rmst() on ertte_coxph returns a tidy tibble with sane RMST values ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_rmst(mod, ertte_data[1:5, ], tau = c(30, 60, 90)) at test-ertte-rmst.R:18:3
2. └─ertte:::ertte_rmst.ertte_coxph(...)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:32:3'): ertte_rmst() on ertte_coxph matches a hand-computed step-function integral ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_rmst(mod, prof, tau = tau) at test-ertte-rmst.R:32:3
2. └─ertte:::ertte_rmst.ertte_coxph(mod, prof, tau = tau)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:53:3'): ertte_rmst()'s Cox SE is not just the population-level Greenwood term ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_rmst(mod, prof_hi, tau = tau) at test-ertte-rmst.R:53:3
2. └─ertte:::ertte_rmst.ertte_coxph(mod, prof_hi, tau = tau)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:91:3'): ertte_rmst() defaults newdata to the fitted data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(ertte_rmst(mod_cox, tau = 90)), nrow(ertte_data)) at test-ertte-rmst.R:91:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(ertte_rmst(mod_cox, tau = 90))
5. ├─ertte::ertte_rmst(mod_cox, tau = 90)
6. └─ertte:::ertte_rmst.ertte_coxph(mod_cox, tau = 90)
7. ├─survival::survfit(...)
8. └─survival:::survfit.coxph(...)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:106:3'): ertte_rmst() on ertte_coxph warns when tau exceeds the observed follow-up range ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-ertte-rmst.R:106:3
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. ├─ertte::ertte_rmst(...)
8. └─ertte:::ertte_rmst.ertte_coxph(...)
9. ├─survival::survfit(...)
10. └─survival:::survfit.coxph(...)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:125:3'): ertte_rmst() handles a single-row newdata for both engines ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ertte-rmst.R:125:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(ertte_rmst(mod_cox, nd, tau = c(30, 60, 90)))
5. ├─ertte::ertte_rmst(mod_cox, nd, tau = c(30, 60, 90))
6. └─ertte:::ertte_rmst.ertte_coxph(mod_cox, nd, tau = c(30, 60, 90))
7. ├─survival::survfit(...)
8. └─survival:::survfit.coxph(...)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-ertte-rmst.R:174:5'): ertte_rmst() recomputes fit_rmst/ci_lower/ci_upper even when newdata already has columns of those names ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─ertte::ertte_rmst(mod, grid, tau = 90) at test-ertte-rmst.R:174:5
2. └─ertte:::ertte_rmst.ertte_coxph(mod, grid, tau = 90)
3. ├─survival::survfit(...)
4. └─survival:::survfit.coxph(...)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 36 | WARN 1 | SKIP 0 | PASS 293 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc