Last updated on 2026-10-23 06:54:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.5 | 16.14 | 387.45 | 403.59 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.5 | 12.53 | 254.68 | 267.21 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.5 | 12.00 | 239.38 | 251.38 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.5 | 11.00 | 232.20 | 243.20 | ERROR | |
| r-devel-windows-x86_64 | 0.3.5 | 18.00 | 339.00 | 357.00 | OK | |
| r-patched-linux-x86_64 | 0.3.5 | 14.04 | 372.57 | 386.61 | OK | |
| r-release-linux-x86_64 | 0.3.5 | 14.71 | 373.35 | 388.06 | OK | |
| r-release-macos-arm64 | 0.3.5 | 4.00 | 85.00 | 89.00 | OK | |
| r-release-macos-x86_64 | 0.3.5 | 11.00 | 338.00 | 349.00 | OK | |
| r-release-windows-x86_64 | 0.3.5 | 17.00 | 330.00 | 347.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.5 | 4.00 | 84.00 | 88.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.5 | 11.00 | 359.00 | 370.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.5 | 24.00 | 476.00 | 500.00 | OK |
Version: 0.3.5
Check: examples
Result: ERROR
Running examples in ‘censored-Ex.R’ failed
The error most likely occurred in:
> ### Name: censored-package
> ### Title: censored: parsnip Engines for Survival Models
> ### Aliases: censored censored-package
>
> ### ** Examples
>
> # Accelerated Failure Time (AFT) model
>
> fit_aft <- survival_reg(dist = "weibull") |>
+ set_engine("survival") |>
+ fit(Surv(time, status) ~ age + sex + ph.karno, data = lung)
> predict(fit_aft, lung[1:3, ], type = "time")
# A tibble: 3 × 1
.pred_time
<dbl>
1 355.
2 374.
3 416.
>
>
> # Cox's Proportional Hazards model
>
> fit_cox <- proportional_hazards() |>
+ set_engine("survival") |>
+ fit(Surv(time, status) ~ age + sex + ph.karno, data = lung)
> predict(fit_cox, lung[1:3, ], type = "time")
Error in a$specials[[i]] : subscript out of bounds
Calls: predict ... <Anonymous> -> get_missings_coxph -> <Anonymous> -> off
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [147s/262s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(censored)
Loading required package: parsnip
Loading required package: survival
>
> test_check("censored")
Saving _problems/test-aaa_survival_prob-6.R
Saving _problems/test-aaa_survival_prob-43.R
Saving _problems/test-aaa_survival_prob-88.R
Saving _problems/test-aaa_survival_prob-149.R
Saving _problems/test-aaa_survival_prob-193.R
Saving _problems/test-boost_tree-mboost-128.R
Saving _problems/test-decision_tree-rpart-7.R
Saving _problems/test-decision_tree-rpart-28.R
Saving _problems/test-decision_tree-rpart-56.R
Saving _problems/test-decision_tree-rpart-120.R
Saving _problems/test-decision_tree-rpart-136.R
Saving _problems/test-decision_tree-rpart-161.R
Saving _problems/test-proportional_hazards-glmnet-44.R
Saving _problems/test-proportional_hazards-glmnet-92.R
Saving _problems/test-proportional_hazards-glmnet-145.R
Saving _problems/test-proportional_hazards-glmnet-190.R
Saving _problems/test-proportional_hazards-glmnet-240.R
Saving _problems/test-proportional_hazards-glmnet-317.R
Saving _problems/test-proportional_hazards-glmnet-429.R
Saving _problems/test-proportional_hazards-glmnet-437.R
Saving _problems/test-proportional_hazards-glmnet-535.R
Saving _problems/test-proportional_hazards-glmnet-637.R
Saving _problems/test-proportional_hazards-glmnet-638.R
Saving _problems/test-proportional_hazards-glmnet-727.R
Saving _problems/test-proportional_hazards-glmnet-728.R
Saving _problems/test-proportional_hazards-glmnet-818.R
Saving _problems/test-proportional_hazards-glmnet-902.R
Saving _problems/test-proportional_hazards-glmnet-1000.R
Saving _problems/test-proportional_hazards-glmnet-1289.R
Saving _problems/test-proportional_hazards-glmnet-1322.R
Saving _problems/test-proportional_hazards-glmnet-1358.R
Saving _problems/test-proportional_hazards-glmnet-1412.R
Saving _problems/test-proportional_hazards-glmnet-1454.R
Saving _problems/test-proportional_hazards-glmnet-1497.R
Saving _problems/test-proportional_hazards-glmnet-1626.R
Saving _problems/test-proportional_hazards-glmnet-1668.R
Saving _problems/test-proportional_hazards-glmnet-1711.R
Saving _problems/test-proportional_hazards-glmnet-1820.R
Saving _problems/test-proportional_hazards-glmnet-1847.R
Saving _problems/test-proportional_hazards-survival-29.R
Saving _problems/test-proportional_hazards-survival-61.R
Saving _problems/test-proportional_hazards-survival-99.R
Saving _problems/test-proportional_hazards-survival-100.R
Saving _problems/test-proportional_hazards-survival-172.R
Saving _problems/test-proportional_hazards-survival-246.R
Saving _problems/test-proportional_hazards-survival-328.R
Saving _problems/test-proportional_hazards-survival-329.R
Saving _problems/test-proportional_hazards-survival-400.R
Saving _problems/test-proportional_hazards-survival-444.R
Saving _problems/test-proportional_hazards-survival-489.R
Saving _problems/test-proportional_hazards-survival-502.R
Saving _problems/test-proportional_hazards-survival-537.R
Saving _problems/test-proportional_hazards-survival-585.R
Saving _problems/test-proportional_hazards-survival-589.R
Saving _problems/test-proportional_hazards-survival-611.R
Saving _problems/test-proportional_hazards-survival-702.R
Saving _problems/test-proportional_hazards-survival-747.R
Saving _problems/test-proportional_hazards-survival-835.R
Saving _problems/test-proportional_hazards-survival-880.R
Saving _problems/test-survival_reg-flexsurvspline-11.R
Saving _problems/test-survival_reg-flexsurvspline-39.R
Saving _problems/test-survival_reg-flexsurvspline-63.R
Saving _problems/test-survival_reg-flexsurvspline-151.R
Saving _problems/test-survival_reg-flexsurvspline-182.R
Saving _problems/test-survival_reg-flexsurvspline-209.R
Saving _problems/test-survival_reg-flexsurvspline-238.R
Saving _problems/test-survival_reg-flexsurvspline-305.R
Saving _problems/test-survival_reg-flexsurvspline-371.R
Saving _problems/test-survival_reg-flexsurvspline-407.R
Saving _problems/test-survival_reg-flexsurvspline-492.R
Saving _problems/test-survival_reg-flexsurvspline-499.R
[ FAIL 71 | WARN 26 | SKIP 17 | PASS 295 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-bag_tree-rpart.R:63:1', 'test-bag_tree-rpart.R:127:1',
'test-boost_tree-mboost.R:108:1', 'test-decision_tree-partykit.R:113:1',
'test-proportional_hazards-glmnet.R:23:1',
'test-proportional_hazards-glmnet.R:1204:1',
'test-proportional_hazards-glmnet.R:1216:1',
'test-proportional_hazards-glmnet.R:1247:1',
'test-proportional_hazards-glmnet.R:1381:1',
'test-proportional_hazards-survival.R:134:1',
'test-proportional_hazards-survival.R:211:1',
'test-proportional_hazards.R:4:1', 'test-rand_forest-aorsf.R:210:1',
'test-rand_forest-partykit.R:134:1', 'test-survival_reg-survival.R:47:1',
'test-survival_reg-survival.R:189:1', 'test-survival_reg.R:4:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aaa_survival_prob.R:6:3'): survfit_summary_typestable() works for survival prob - unstratified (coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:6:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:43:3'): survfit_summary_typestable() works for survival prob - stratified (coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:43:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:88:3'): survfit_summary_typestable() works for survival prob - unstratified (coxnet) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-aaa_survival_prob.R:88:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-aaa_survival_prob.R:142:3'): survfit_summary_typestable() works for survival prob - stratified (coxnet) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-aaa_survival_prob.R:142:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:193:3'): survfit_summary_patch_missings() works ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:193:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-boost_tree-mboost.R:128:3'): survival_curve_to_prob() works ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-boost_tree-mboost.R:128:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:7:3'): model object ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:7:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:28:3'): time predictions ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:28:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:56:3'): survival predictions ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:56:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:120:3'): survival predictions - error snapshot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(cox_spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:120:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ age + ph.ecog, data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:133:3'): can predict for out-of-domain timepoints ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-decision_tree-rpart.R:133:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ ., data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:161:3'): `fix_xy()` works ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:161:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ age + ph.ecog, data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:44:3'): time predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:44:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:85:3'): time predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:85:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:145:3'): time predictions with NA in predictor ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, na_x_data_x, type = "time") at test-proportional_hazards-glmnet.R:145:3
2. ├─censored:::predict._coxnet(f_fit, na_x_data_x, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:190:3'): time predictions with NA in strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, na_x_data_x, type = "time") at test-proportional_hazards-glmnet.R:190:3
2. ├─censored:::predict._coxnet(f_fit, na_x_data_x, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:234:3'): survival_time_coxnet() works for single penalty value ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:234:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:311:3'): survival_time_coxnet() works for multiple penalty values ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:311:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:422:3'): survival probabilities without strata ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:431:3'): survival probabilities without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-glmnet.R:431:3
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:529:3'): survival probabilities with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-glmnet.R:529:3
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:630:3'): survival prediction with NA in predictor ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:638:3'): survival prediction with NA in predictor ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-glmnet.R:638:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Failure ('test-proportional_hazards-glmnet.R:720:3'): survival prediction with NA in strata ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:728:3'): survival prediction with NA in strata ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-glmnet.R:728:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-glmnet.R:812:3'): survival_prob_coxnet() works for single penalty value ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:812:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:896:3'): survival_prob_coxnet() works for multiple penalty values ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:896:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:993:3'): can predict for out-of-domain timepoints ──
Expected `preds <- predict(mod, obs_without_NA, type = "survival", eval_time = eval_time_obs_max_and_ood)` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:1286:3'): predictions with strata and dot in formula ──
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...)
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1322:3'): `fit_xy()` works with matrix input ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-glmnet.R:1322:3
2. ├─censored:::predict._coxnet(f_fit, new_data = lung_pred, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1358:3'): `fit_xy()` works with data frame input ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-glmnet.R:1358:3
2. ├─censored:::predict._coxnet(f_fit, new_data = lung_pred, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1407:3'): multi_predict(type = time) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1407:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1448:3'): multi_predict(type = survival) for multiple eval_time points ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1448:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1491:3'): multi_predict(type = survival) for a single eval_time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1491:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1621:3'): multi_predict(type = time) works with single penalty ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1621:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1662:3'): multi_predict(type = survival) works with single penalty for multiple eval_time points ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1662:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1705:3'): multi_predict(type = survival) works with single penalty for a single eval_time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1705:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1815:3'): multi_predict(): type = NULL ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1815:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1842:3'): multi_predict() recognises default penalty ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1842:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:29:3'): time predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "time") at test-proportional_hazards-survival.R:29:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:61:3'): time predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data_3, type = "time") at test-proportional_hazards-survival.R:61:3
2. ├─parsnip::predict.model_fit(f_fit, new_data_3, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:97:3'): time predictions with NA ──
Expected `f_pred <- predict(f_fit, na_x_data_x, type = "time")` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:100:3'): time predictions with NA ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-survival.R:100:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-survival.R:172:3'): survival predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:172:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:241:3'): survival predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:241:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:321:3'): survival prediction with NA ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:329:3'): survival prediction with NA ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-survival.R:329:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-survival.R:400:3'): survival_prob_coxph() works ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod$fit, newdata = lung_pred) at test-proportional_hazards-survival.R:400:3
2. └─survival:::survfit.coxph(mod$fit, newdata = lung_pred)
3. └─stats::delete.response(Terms)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:444:3'): survival_prob_coxph() works with confidence intervals ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod$fit, newdata = lung_pred) at test-proportional_hazards-survival.R:444:3
2. └─survival:::survfit.coxph(mod$fit, newdata = lung_pred)
3. └─stats::delete.response(Terms)
4. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:482:3'): can predict for out-of-domain timepoints ──
Expected `preds <- predict(mod, obs_without_NA, type = "survival", eval_time = eval_time_obs_max_and_ood)` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:502:3'): linear_pred predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "linear_pred") at test-proportional_hazards-survival.R:502:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "linear_pred")
3. │ ├─parsnip::predict_linear_pred(...)
4. │ ├─censored:::predict_linear_pred._coxph(...)
5. │ ├─base::NextMethod()
6. │ └─parsnip::predict_linear_pred.model_fit(...)
7. │ └─rlang::eval_tidy(pred_call)
8. ├─stats::predict(...)
9. └─survival:::predict.coxph(...)
10. └─stats::delete.response(Terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:537:3'): linear_pred predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "linear_pred") at test-proportional_hazards-survival.R:537:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "linear_pred")
3. │ ├─parsnip::predict_linear_pred(...)
4. │ ├─censored:::predict_linear_pred._coxph(...)
5. │ ├─base::NextMethod()
6. │ └─parsnip::predict_linear_pred.model_fit(...)
7. │ └─rlang::eval_tidy(pred_call)
8. ├─stats::predict(...)
9. └─survival:::predict.coxph(...)
10. └─stats::delete.response(Terms)
11. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:579:3'): predictions with strata and dot in formula ──
Expected `{ ... }` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:586:3'): predictions with strata and dot in formula ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:586:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(f_fit, lung2, type = "time")
5. ├─parsnip::predict.model_fit(f_fit, lung2, type = "time")
6. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
7. │ └─parsnip::predict_time.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_time_coxph(object = object, new_data = new_data)
10. └─censored:::get_missings_coxph(object$fit, new_data)
11. └─stats::delete.response(trms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:605:3'): confidence intervals ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:605:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:699:3'): get_missings_coxph() can identify missings without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:699:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:744:3'): get_missings_coxph() can identify missings with single strata term ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:744:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:832:3'): get_missings_coxph() can identify missings with two strata terms ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:832:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:880:3'): `fix_xy()` works ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-survival.R:880:3
2. ├─parsnip::predict.model_fit(f_fit, new_data = lung_pred, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:7:3'): model object ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:7:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:35:3'): time prediction ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:35:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:59:3'): survival probability prediction ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:59:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:150:3'): survival probabilities for single eval time point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:150:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:179:3'): can predict for out-of-domain timepoints ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:179:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(formula = Surv(time, status) ~ ., data = data)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:207:3'): linear predictor ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:207:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:235:3'): quantile predictions ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:235:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:301:3'): hazard prediction ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:301:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:370:3'): hazard for single eval time point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:370:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:407:3'): `fix_xy()` works ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-survival_reg-flexsurvspline.R:407:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Failure ('test-survival_reg-flexsurvspline.R:486:3'): can handle case weights ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-survival_reg-flexsurvspline.R:494:3'): can handle case weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-survival_reg-flexsurvspline.R:494:3
2. │ └─base::withCallingHandlers(...)
3. ├─generics::fit(...)
4. ├─parsnip::fit.model_spec(...)
5. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
6. │ └─parsnip:::eval_mod(...)
7. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
8. │ └─rlang::eval_tidy(e, env = envir)
9. └─flexsurv::flexsurvspline(...)
10. ├─base::do.call("flexsurvreg", args)
11. └─flexsurv::flexsurvreg(...)
12. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
13. ├─survival::survfit(cox, newdata = newdata)
14. └─survival:::survfit.coxph(cox, newdata = newdata)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
[ FAIL 71 | WARN 26 | SKIP 17 | PASS 295 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [144s/265s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(censored)
Loading required package: parsnip
Loading required package: survival
>
> test_check("censored")
Saving _problems/test-aaa_survival_prob-6.R
Saving _problems/test-aaa_survival_prob-43.R
Saving _problems/test-aaa_survival_prob-88.R
Saving _problems/test-aaa_survival_prob-149.R
Saving _problems/test-aaa_survival_prob-193.R
Saving _problems/test-boost_tree-mboost-128.R
Saving _problems/test-decision_tree-rpart-7.R
Saving _problems/test-decision_tree-rpart-28.R
Saving _problems/test-decision_tree-rpart-56.R
Saving _problems/test-decision_tree-rpart-120.R
Saving _problems/test-decision_tree-rpart-136.R
Saving _problems/test-decision_tree-rpart-161.R
Saving _problems/test-proportional_hazards-glmnet-44.R
Saving _problems/test-proportional_hazards-glmnet-92.R
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Saving _problems/test-proportional_hazards-glmnet-1847.R
Saving _problems/test-proportional_hazards-survival-29.R
Saving _problems/test-proportional_hazards-survival-61.R
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Saving _problems/test-proportional_hazards-survival-747.R
Saving _problems/test-proportional_hazards-survival-835.R
Saving _problems/test-proportional_hazards-survival-880.R
Saving _problems/test-survival_reg-flexsurvspline-11.R
Saving _problems/test-survival_reg-flexsurvspline-39.R
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Saving _problems/test-survival_reg-flexsurvspline-151.R
Saving _problems/test-survival_reg-flexsurvspline-182.R
Saving _problems/test-survival_reg-flexsurvspline-209.R
Saving _problems/test-survival_reg-flexsurvspline-238.R
Saving _problems/test-survival_reg-flexsurvspline-305.R
Saving _problems/test-survival_reg-flexsurvspline-371.R
Saving _problems/test-survival_reg-flexsurvspline-407.R
Saving _problems/test-survival_reg-flexsurvspline-492.R
Saving _problems/test-survival_reg-flexsurvspline-499.R
[ FAIL 71 | WARN 26 | SKIP 17 | PASS 295 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-bag_tree-rpart.R:63:1', 'test-bag_tree-rpart.R:127:1',
'test-boost_tree-mboost.R:108:1', 'test-decision_tree-partykit.R:113:1',
'test-proportional_hazards-glmnet.R:23:1',
'test-proportional_hazards-glmnet.R:1204:1',
'test-proportional_hazards-glmnet.R:1216:1',
'test-proportional_hazards-glmnet.R:1247:1',
'test-proportional_hazards-glmnet.R:1381:1',
'test-proportional_hazards-survival.R:134:1',
'test-proportional_hazards-survival.R:211:1',
'test-proportional_hazards.R:4:1', 'test-rand_forest-aorsf.R:210:1',
'test-rand_forest-partykit.R:134:1', 'test-survival_reg-survival.R:47:1',
'test-survival_reg-survival.R:189:1', 'test-survival_reg.R:4:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aaa_survival_prob.R:6:3'): survfit_summary_typestable() works for survival prob - unstratified (coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:6:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:43:3'): survfit_summary_typestable() works for survival prob - stratified (coxph) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:43:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:88:3'): survfit_summary_typestable() works for survival prob - unstratified (coxnet) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-aaa_survival_prob.R:88:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-aaa_survival_prob.R:142:3'): survfit_summary_typestable() works for survival prob - stratified (coxnet) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-aaa_survival_prob.R:142:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-aaa_survival_prob.R:193:3'): survfit_summary_patch_missings() works ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-aaa_survival_prob.R:193:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-boost_tree-mboost.R:128:3'): survival_curve_to_prob() works ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod, newdata = lung_pred) at test-boost_tree-mboost.R:128:3
2. └─survival:::survfit.coxph(mod, newdata = lung_pred)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:7:3'): model object ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:7:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:28:3'): time predictions ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:28:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:56:3'): survival predictions ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pecRpart(Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:56:3
2. └─prodlim::prodlim(form, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:120:3'): survival predictions - error snapshot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(cox_spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:120:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ age + ph.ecog, data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:133:3'): can predict for out-of-domain timepoints ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-decision_tree-rpart.R:133:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ ., data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-decision_tree-rpart.R:161:3'): `fix_xy()` works ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-decision_tree-rpart.R:161:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─pec::pecRpart(formula = Surv(time, status) ~ age + ph.ecog, data = data)
8. └─prodlim::prodlim(form, data = data)
9. └─prodlim::EventHistory.frame(...)
10. └─prodlim::model.design(...)
11. └─stats::delete.response(terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:44:3'): time predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:44:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:85:3'): time predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:85:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:145:3'): time predictions with NA in predictor ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, na_x_data_x, type = "time") at test-proportional_hazards-glmnet.R:145:3
2. ├─censored:::predict._coxnet(f_fit, na_x_data_x, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:190:3'): time predictions with NA in strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, na_x_data_x, type = "time") at test-proportional_hazards-glmnet.R:190:3
2. ├─censored:::predict._coxnet(f_fit, na_x_data_x, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:234:3'): survival_time_coxnet() works for single penalty value ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:234:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:311:3'): survival_time_coxnet() works for multiple penalty values ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:311:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:422:3'): survival probabilities without strata ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:431:3'): survival probabilities without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-glmnet.R:431:3
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:529:3'): survival probabilities with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-glmnet.R:529:3
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:630:3'): survival prediction with NA in predictor ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:638:3'): survival prediction with NA in predictor ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-glmnet.R:638:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Failure ('test-proportional_hazards-glmnet.R:720:3'): survival prediction with NA in strata ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:728:3'): survival prediction with NA in strata ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-glmnet.R:728:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-glmnet.R:812:3'): survival_prob_coxnet() works for single penalty value ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:812:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
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-proportional_hazards-glmnet.R:896:3'): survival_prob_coxnet() works for multiple penalty values ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(...) at test-proportional_hazards-glmnet.R:896:3
2. └─glmnet:::survfit.coxnet(...)
3. ├─base::do.call(survfit, current_args)
4. ├─survival (local) `<fn>`(...)
5. └─survival:::survfit.coxph(...)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-glmnet.R:993:3'): can predict for out-of-domain timepoints ──
Expected `preds <- predict(mod, obs_without_NA, type = "survival", eval_time = eval_time_obs_max_and_ood)` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-glmnet.R:1286:3'): predictions with strata and dot in formula ──
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...)
2. ├─censored:::predict._coxnet(...)
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_survival(...)
5. │ ├─censored:::predict_survival._coxnet(...)
6. │ ├─base::NextMethod()
7. │ └─parsnip::predict_survival.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_prob_coxnet(...)
10. ├─survival::survfit(...)
11. └─glmnet:::survfit.coxnet(...)
12. ├─base::do.call(survfit, current_args)
13. ├─survival (local) `<fn>`(...)
14. └─survival:::survfit.coxph(...)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1322:3'): `fit_xy()` works with matrix input ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-glmnet.R:1322:3
2. ├─censored:::predict._coxnet(f_fit, new_data = lung_pred, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1358:3'): `fit_xy()` works with data frame input ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-glmnet.R:1358:3
2. ├─censored:::predict._coxnet(f_fit, new_data = lung_pred, type = "time")
3. │ └─parsnip::predict.model_fit(...)
4. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
5. │ └─parsnip::predict_time.model_fit(...)
6. │ └─rlang::eval_tidy(pred_call)
7. └─censored::survival_time_coxnet(...)
8. ├─survival::survfit(...)
9. └─glmnet:::survfit.coxnet(...)
10. ├─base::do.call(survfit, current_args)
11. ├─survival (local) `<fn>`(...)
12. └─survival:::survfit.coxph(...)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1407:3'): multi_predict(type = time) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1407:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1448:3'): multi_predict(type = survival) for multiple eval_time points ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1448:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1491:3'): multi_predict(type = survival) for a single eval_time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1491:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1621:3'): multi_predict(type = time) works with single penalty ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1621:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1662:3'): multi_predict(type = survival) works with single penalty for multiple eval_time points ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1662:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1705:3'): multi_predict(type = survival) works with single penalty for a single eval_time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1705:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1815:3'): multi_predict(): type = NULL ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1815:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_time(...)
4. └─censored::survival_time_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-glmnet.R:1842:3'): multi_predict() recognises default penalty ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─parsnip::multi_predict(...) at test-proportional_hazards-glmnet.R:1842:3
2. └─censored:::multi_predict._coxnet(...)
3. └─censored:::multi_predict_coxnet_survival(...)
4. └─censored::survival_prob_coxnet(...)
5. ├─survival::survfit(...)
6. └─glmnet:::survfit.coxnet(...)
7. ├─base::do.call(survfit, current_args)
8. ├─survival (local) `<fn>`(...)
9. └─survival:::survfit.coxph(...)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:29:3'): time predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "time") at test-proportional_hazards-survival.R:29:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:61:3'): time predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data_3, type = "time") at test-proportional_hazards-survival.R:61:3
2. ├─parsnip::predict.model_fit(f_fit, new_data_3, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:97:3'): time predictions with NA ──
Expected `f_pred <- predict(f_fit, na_x_data_x, type = "time")` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:100:3'): time predictions with NA ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-survival.R:100:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-survival.R:172:3'): survival predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:172:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:241:3'): survival predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:241:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:321:3'): survival prediction with NA ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:329:3'): survival prediction with NA ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'f_pred' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(f_pred), nrow(na_x_data_x)) at test-proportional_hazards-survival.R:329:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::nrow(f_pred)
── Error ('test-proportional_hazards-survival.R:400:3'): survival_prob_coxph() works ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod$fit, newdata = lung_pred) at test-proportional_hazards-survival.R:400:3
2. └─survival:::survfit.coxph(mod$fit, newdata = lung_pred)
3. └─stats::delete.response(Terms)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:444:3'): survival_prob_coxph() works with confidence intervals ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(mod$fit, newdata = lung_pred) at test-proportional_hazards-survival.R:444:3
2. └─survival:::survfit.coxph(mod$fit, newdata = lung_pred)
3. └─stats::delete.response(Terms)
4. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:482:3'): can predict for out-of-domain timepoints ──
Expected `preds <- predict(mod, obs_without_NA, type = "survival", eval_time = eval_time_obs_max_and_ood)` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:502:3'): linear_pred predictions without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "linear_pred") at test-proportional_hazards-survival.R:502:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "linear_pred")
3. │ ├─parsnip::predict_linear_pred(...)
4. │ ├─censored:::predict_linear_pred._coxph(...)
5. │ ├─base::NextMethod()
6. │ └─parsnip::predict_linear_pred.model_fit(...)
7. │ └─rlang::eval_tidy(pred_call)
8. ├─stats::predict(...)
9. └─survival:::predict.coxph(...)
10. └─stats::delete.response(Terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:537:3'): linear_pred predictions with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, lung, type = "linear_pred") at test-proportional_hazards-survival.R:537:3
2. ├─parsnip::predict.model_fit(f_fit, lung, type = "linear_pred")
3. │ ├─parsnip::predict_linear_pred(...)
4. │ ├─censored:::predict_linear_pred._coxph(...)
5. │ ├─base::NextMethod()
6. │ └─parsnip::predict_linear_pred.model_fit(...)
7. │ └─rlang::eval_tidy(pred_call)
8. ├─stats::predict(...)
9. └─survival:::predict.coxph(...)
10. └─stats::delete.response(Terms)
11. └─stats (local) off(a$specials[[i]])
── Failure ('test-proportional_hazards-survival.R:579:3'): predictions with strata and dot in formula ──
Expected `{ ... }` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-proportional_hazards-survival.R:586:3'): predictions with strata and dot in formula ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:586:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─stats::predict(f_fit, lung2, type = "time")
5. ├─parsnip::predict.model_fit(f_fit, lung2, type = "time")
6. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
7. │ └─parsnip::predict_time.model_fit(...)
8. │ └─rlang::eval_tidy(pred_call)
9. └─censored::survival_time_coxph(object = object, new_data = new_data)
10. └─censored:::get_missings_coxph(object$fit, new_data)
11. └─stats::delete.response(trms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:605:3'): confidence intervals ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(...) at test-proportional_hazards-survival.R:605:3
2. ├─parsnip::predict.model_fit(...)
3. │ ├─parsnip::predict_survival(...)
4. │ └─parsnip::predict_survival.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_prob_coxph(...)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:699:3'): get_missings_coxph() can identify missings without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:699:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:744:3'): get_missings_coxph() can identify missings with single strata term ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:744:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:832:3'): get_missings_coxph() can identify missings with two strata terms ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-proportional_hazards-survival.R:832:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unname(unclass(get_missings_coxph(f_fit$fit, na_x_data_x)))
5. └─censored:::get_missings_coxph(f_fit$fit, na_x_data_x)
6. └─stats::delete.response(trms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-proportional_hazards-survival.R:880:3'): `fix_xy()` works ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(f_fit, new_data = lung_pred, type = "time") at test-proportional_hazards-survival.R:880:3
2. ├─parsnip::predict.model_fit(f_fit, new_data = lung_pred, type = "time")
3. │ ├─parsnip::predict_time(object = object, new_data = new_data, ...)
4. │ └─parsnip::predict_time.model_fit(...)
5. │ └─rlang::eval_tidy(pred_call)
6. └─censored::survival_time_coxph(object = object, new_data = new_data)
7. └─censored:::get_missings_coxph(object$fit, new_data)
8. └─stats::delete.response(trms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:7:3'): model object ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:7:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:35:3'): time prediction ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:35:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:59:3'): survival probability prediction ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:59:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:150:3'): survival probabilities for single eval time point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:150:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:179:3'): can predict for out-of-domain timepoints ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:179:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(formula = Surv(time, status) ~ ., data = data)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:207:3'): linear predictor ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:207:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:235:3'): quantile predictions ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:235:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:301:3'): hazard prediction ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-survival_reg-flexsurvspline.R:301:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:370:3'): hazard for single eval time point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(...) at test-survival_reg-flexsurvspline.R:370:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test-survival_reg-flexsurvspline.R:407:3'): `fix_xy()` works ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─generics::fit(spec, Surv(time, status) ~ age + ph.ecog, data = lung) at test-survival_reg-flexsurvspline.R:407:3
2. ├─parsnip::fit.model_spec(...)
3. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
4. │ └─parsnip:::eval_mod(...)
5. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
6. │ └─rlang::eval_tidy(e, env = envir)
7. └─flexsurv::flexsurvspline(...)
8. ├─base::do.call("flexsurvreg", args)
9. └─flexsurv::flexsurvreg(...)
10. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
11. ├─survival::survfit(cox, newdata = newdata)
12. └─survival:::survfit.coxph(cox, newdata = newdata)
13. └─survival:::model.matrix.coxph(object, data = mf)
14. └─stats::delete.response(object$terms)
15. └─stats (local) off(a$specials[[i]])
── Failure ('test-survival_reg-flexsurvspline.R:486:3'): can handle case weights ──
Expected `... <- NULL` not to throw any errors.
Actually got a <subscriptOutOfBoundsError> with message:
subscript out of bounds
── Error ('test-survival_reg-flexsurvspline.R:494:3'): can handle case weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-survival_reg-flexsurvspline.R:494:3
2. │ └─base::withCallingHandlers(...)
3. ├─generics::fit(...)
4. ├─parsnip::fit.model_spec(...)
5. │ └─parsnip:::form_form(object = object, control = control, env = eval_env)
6. │ └─parsnip:::eval_mod(...)
7. │ └─parsnip:::eval_mod_catch(e, catch = catch, envir = envir)
8. │ └─rlang::eval_tidy(e, env = envir)
9. └─flexsurv::flexsurvspline(...)
10. ├─base::do.call("flexsurvreg", args)
11. └─flexsurv::flexsurvreg(...)
12. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
13. ├─survival::survfit(cox, newdata = newdata)
14. └─survival:::survfit.coxph(cox, newdata = newdata)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
[ FAIL 71 | WARN 26 | SKIP 17 | PASS 295 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc