Last updated on 2026-10-24 09:50:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 13.28 | 202.28 | 215.56 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 8.58 | 124.58 | 133.16 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 139.57 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 141.04 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 15.00 | 199.00 | 214.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 13.12 | 187.57 | 200.69 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 13.03 | 193.57 | 206.60 | OK | |
| r-release-macos-arm64 | 0.2.0 | 3.00 | 50.00 | 53.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 10.00 | 227.00 | 237.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 14.00 | 191.00 | 205.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 4.00 | 68.00 | 72.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.0 | 10.00 | 208.00 | 218.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 22.00 | 255.00 | 277.00 | OK |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘BJM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.survivalSub.BJM
> ### Title: Summary method for 'survivalSub.BJM' objects
> ### Aliases: summary.survivalSub.BJM
>
> ### ** Examples
>
> data(pbc3)
> data_survival_fitting <- pbc3[!duplicated(pbc3$id), ]
> form_marginal_surv <- Surv(years, status3) ~ age + sex
> form_conditional_cr <- status4 ~ years + age + sex
> survival_fit_all <- survivalSub(data_survival_fitting,
+ form_marginal_surv, form_conditional_cr)
> summary(survival_fit_all)
Call:
survivalSub(form_marginal_surv = Surv(years, status3) ~ age + sex,
form_conditional_cr = status4 ~ years + age + sex)
Data Descriptives:
Number of subjects : 312
Number of events : 169
Cause-1 events (CR model) : 29
Cause-2 events (CR model) : 140
=================================================================
Marginal Survival Sub-model [Cox PH]
-----------------------------------------------------------------
Formula: Surv(years, status3) ~ age + sex
Coef exp(Coef) SE z p-value
age 0.020411 1.020621 0.007584 2.691 0.00712 **
sex -0.497707 0.607923 0.207078 -2.403 0.01624 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
n = 312, events = 169
Concordance = 0.570 (se = 0.0226)
Likelihood ratio = 14.20 on 2 df, p = 0.0008263
Wald test = 15.29 on 2 df, p = 0.0004776
Score (logrank) = 15.50 on 2 df, p = 0.0004299
Error in a$specials[[i]] : subscript out of bounds
Calls: summary ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [42s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BJM)
Loading required package: survival
>
> test_check("BJM")
Saving _problems/test-autoBandcount-72.R
Saving _problems/test-autoBandcount-85.R
Saving _problems/test-autoBandcount-97.R
Tracing function "dynamicPrediction" in package "namespace:BJM"
Saving _problems/test-autoBandcount-120.R
Saving _problems/test-autoBandcount-137.R
Saving _problems/test-checkBandcountConvergence-61.R
Saving _problems/test-checkBandcountConvergence-81.R
Saving _problems/test-checkBandcountConvergence-96.R
Saving _problems/test-dynamicPrediction-10.R
Saving _problems/test-dynamicPrediction-37.R
Saving _problems/test-dynamicPrediction-51.R
Saving _problems/test-input-validation-85.R
Saving _problems/test-usability-helpers-31.R
[ FAIL 14 | WARN 0 | SKIP 2 | PASS 73 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-baseline-characterization-noCR.R:12:3',
'test-baseline-characterization.R:14:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoBandcount.R:68:3'): dynamicPrediction defaults to auto bandcount1/bandcount2 and returns valid risk probabilities ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-autoBandcount.R:68:3
2. │ └─base::withCallingHandlers(...)
3. └─BJM::dynamicPrediction(...)
4. └─BJM:::auto_tune_bandcount(dynamicPrediction, call_args, auto_names)
5. ├─base::do.call(predict_fun, args)
6. └─BJM (local) `<fn>`(...)
7. └─BJM:::prepare_infinity_grid(...)
8. └─BJM:::marginalT(...)
9. └─survival::basehaz(coxph_fit, centered = FALSE)
10. ├─survival::survfit(fit, se.fit = FALSE)
11. └─survival:::survfit.coxph(fit, se.fit = FALSE)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-autoBandcount.R:82:3'): dynamicPrediction with explicit numeric bandcount1/bandcount2 still bypasses auto-tuning (backward compatible) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPrediction(...) at test-autoBandcount.R:82:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-autoBandcount.R:93:3'): dynamicPredictionBio defaults to auto bandcount2/bandcount3 and returns a MAP estimate ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-autoBandcount.R:93:3
2. │ └─base::withCallingHandlers(...)
3. └─BJM::dynamicPredictionBio(...)
4. └─BJM:::auto_tune_bandcount(dynamicPredictionBio, call_args, auto_names)
5. ├─base::do.call(predict_fun, args)
6. └─BJM (local) `<fn>`(...)
7. └─BJM:::prepare_infinity_grid(...)
8. └─BJM:::marginalT(...)
9. └─survival::basehaz(coxph_fit, centered = FALSE)
10. ├─survival::survfit(fit, se.fit = FALSE)
11. └─survival:::survfit.coxph(fit, se.fit = FALSE)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-autoBandcount.R:115:3'): predictPlot resolves auto bandcount1/bandcount2/bandcount3 once, not per horizon point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-autoBandcount.R:115:3
2. │ └─base::withCallingHandlers(...)
3. └─BJM::predictPlot(...)
4. └─BJM:::auto_tune_bandcount(dynamicPrediction, probe_args, auto_names_1_2)
5. ├─base::do.call(predict_fun, args)
6. └─BJM (local) `<S4: functionWithTrace>`(...)
7. └─BJM:::prepare_infinity_grid(...)
8. └─BJM:::marginalT(...)
9. └─survival::basehaz(coxph_fit, centered = FALSE)
10. ├─survival::survfit(fit, se.fit = FALSE)
11. └─survival:::survfit.coxph(fit, se.fit = FALSE)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-autoBandcount.R:132:3'): riskPlot resolves auto bandcount1/bandcount2 once, not per landmark time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-autoBandcount.R:132:3
2. │ └─base::withCallingHandlers(...)
3. └─BJM::riskPlot(...)
4. └─BJM:::auto_tune_bandcount(dynamicPrediction, probe_args, auto_names_1_2)
5. ├─base::do.call(predict_fun, args)
6. └─BJM (local) `<fn>`(...)
7. └─BJM:::prepare_infinity_grid(...)
8. └─BJM:::marginalT(...)
9. └─survival::basehaz(coxph_fit, centered = FALSE)
10. ├─survival::survfit(fit, se.fit = FALSE)
11. └─survival:::survfit.coxph(fit, se.fit = FALSE)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-checkBandcountConvergence.R:56:3'): checkBandcountConvergence runs dynamicPrediction at base and scaled bandcount1/bandcount2 and compares risk_prob_1/2 ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::checkBandcountConvergence(...) at test-checkBandcountConvergence.R:56:3
2. ├─base::do.call(predict_fun, c(extra_args, bandcount_args))
3. └─BJM (local) `<fn>`(...)
4. └─BJM:::prepare_infinity_grid(...)
5. └─BJM:::marginalT(...)
6. └─survival::basehaz(coxph_fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-checkBandcountConvergence.R:75:3'): checkBandcountConvergence can isolate a single bandcount argument, holding the other fixed via ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::checkBandcountConvergence(...) at test-checkBandcountConvergence.R:75:3
2. ├─base::do.call(predict_fun, c(extra_args, bandcount_args))
3. └─BJM (local) `<fn>`(...)
4. └─BJM:::prepare_infinity_grid(...)
5. └─BJM:::marginalT(...)
6. └─survival::basehaz(coxph_fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-checkBandcountConvergence.R:90:3'): checkBandcountConvergence works with dynamicPredictionBio, comparing Y_predict but not the bandcount3-sized Y_density/Y_all grid ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::checkBandcountConvergence(...) at test-checkBandcountConvergence.R:90:3
2. ├─base::do.call(predict_fun, c(extra_args, bandcount_args))
3. └─BJM (local) `<fn>`(...)
4. └─BJM:::prepare_infinity_grid(...)
5. └─BJM:::marginalT(...)
6. └─survival::basehaz(coxph_fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-dynamicPrediction.R:7:3'): dynamicPrediction returns risk probabilities in [0, 1] with competing risks ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPrediction(...) at test-dynamicPrediction.R:7:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-dynamicPrediction.R:34:3'): dynamicPredictionBio returns a MAP estimate and a density grid ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPredictionBio(...) at test-dynamicPrediction.R:34:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-dynamicPrediction.R:48:3'): print and summary methods run without error ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPrediction(...) at test-dynamicPrediction.R:48:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-input-validation.R:82:3'): dynamicPrediction accepts a bare data.frame for data_predict_all, reusing it for every biomarker ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPrediction(...) at test-input-validation.R:82:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-survivalSub.R:37:3'): print and summary methods run without error ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_output(summary(fit), "Baseline cumulative hazard") at test-survivalSub.R:37:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─base::summary(fit)
11. └─BJM:::summary.survivalSub.BJM(fit)
12. └─BJM:::.format_survivalSub(object, digits = digits, extended = TRUE)
13. └─survival::basehaz(coxph_fit, centered = FALSE)
14. ├─survival::survfit(fit, se.fit = FALSE)
15. └─survival:::survfit.coxph(fit, se.fit = FALSE)
16. └─survival:::model.matrix.coxph(object, data = mf)
17. └─stats::delete.response(object$terms)
18. └─stats (local) off(a$specials[[i]])
── Error ('test-usability-helpers.R:28:3'): dynamicPredictionBio accepts a bare data.frame for data_predict_all ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─BJM::dynamicPredictionBio(...) at test-usability-helpers.R:28:3
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
[ FAIL 14 | WARN 0 | SKIP 2 | PASS 73 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘BJM-intro.Rmd’ using rmarkdown
Quitting from BJM-intro.Rmd:111-131 [dynamic-prediction]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─BJM::dynamicPrediction(...)
2. └─BJM:::prepare_infinity_grid(...)
3. └─BJM:::marginalT(...)
4. └─survival::basehaz(coxph_fit, centered = FALSE)
5. ├─survival::survfit(fit, se.fit = FALSE)
6. └─survival:::survfit.coxph(fit, se.fit = FALSE)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'BJM-intro.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘BJM-intro.Rmd’
SUMMARY: processing the following file failed:
‘BJM-intro.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc