Last updated on 2026-10-24 12:51:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.3 | 6.36 | 633.91 | 640.27 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.3 | 4.48 | 55.20 | 59.68 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.3 | 441.40 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.3 | 455.50 | OK | |||
| r-devel-windows-x86_64 | 1.1.3 | 11.00 | 628.00 | 639.00 | OK | |
| r-patched-linux-x86_64 | 1.1.3 | 6.26 | 633.93 | 640.19 | OK | |
| r-release-linux-x86_64 | 1.1.3 | 5.33 | 634.01 | 639.34 | OK | |
| r-release-macos-arm64 | 1.1.3 | 2.00 | 230.00 | 232.00 | OK | |
| r-release-macos-x86_64 | 1.1.3 | 4.00 | 892.00 | 896.00 | OK | |
| r-release-windows-x86_64 | 1.1.3 | 9.00 | 598.00 | 607.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.3 | 4.00 | 543.00 | 547.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.3 | 12.00 | 842.00 | 854.00 | OK |
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘calibmsm-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_weights
> ### Title: Calculate inverse probability of censoring weights at time 't'.
> ### Aliases: calc_weights
>
> ### ** Examples
>
> # Estimate inverse probability of censoring weights for individual in cohort ebmtcal.
> # Specifically the probability of being uncensored at t = 1826 days.
> # Weights are estimated using a model fitted in all individuals uncensored at time s = 0.
> weights_manual <-
+ calc_weights(data_ms = msebmtcal,
+ data_raw = ebmtcal,
+ covs = c("year", "agecl", "proph", "match"),
+ t = 1826,
+ s = 0,
+ landmark_type = "state",
+ j = 1)
Error in a$specials[[i]] : subscript out of bounds
Calls: calc_weights ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(calibmsm)
>
> test_check("calibmsm")
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_aj-27.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_aj-76.R
Saving _problems/test-calib_blr-23.R
Saving _problems/test-calib_blr-75.R
In the landmark cohort of individuals uncensored and in state j at time s, states {4,5} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_blr-201.R
Saving _problems/test-calib_blr-230.R
Saving _problems/test-calib_blr-379.R
Saving _problems/test-calib_blr-434.R
Saving _problems/test-calib_blr-1016.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_mlr-41.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_mlr-80.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_mlr-114.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-calib_pv-161.R
Saving _problems/test-plot_calib-17.R
Saving _problems/test-plot_calib-60.R
In the landmark cohort of individuals uncensored and in state j at time s, states {4,5} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-plot_calib-96.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-plot_calib-131.R
In the landmark cohort of individuals uncensored and in state j at time s, states {1,2,3,4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-plot_calib-167.R
In the landmark cohort of individuals uncensored and in state j at time s, states {4,5,6} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-plot_calib-204.R
Saving _problems/test-plot_calib-244.R
In the landmark cohort of individuals uncensored and in state j at time s, states {4,5} have less than 30 people in them at the time calibration is being assessed (t).
Warnings and errors may occur when the models to estimate the calibration curves are fitted, due to small sample size.
The number to flag this warning (30) has been chosen arbitrarily, and does not constitute a sufficient sample size from
a statistical point of view.Saving _problems/test-plot_calib-272.R
Saving _problems/test-weights-13.R
Saving _problems/test-weights-53.R
Saving _problems/test-weights-95.R
Saving _problems/test-weights-150.R
Saving _problems/test-weights-190.R
[ FAIL 26 | WARN 0 | SKIP 15 | PASS 14 ]
══ Skipped tests (15) ══════════════════════════════════════════════════════════
• On CRAN (15): 'test-calib_aj.R:106:3', 'test-calib_aj.R:158:3',
'test-calib_blr.R:137:3', 'test-calib_blr.R:267:3',
'test-calib_blr.R:465:13', 'test-calib_blr.R:510:13', 'test-calib_pv.R:10:3',
'test-calib_pv.R:223:3', 'test-calib_pv.R:275:3', 'test-calib_pv.R:328:3',
'test-calib_pv.R:482:3', 'test-calib_pv.R:525:3', 'test-calib_pv.R:556:3',
'test-calib_pv.R:586:3', 'test-calib_pv.R:617:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-calib_aj.R:20:3'): check calib_aj, pv_n_pctls = NULL and pv_group_vars = NULL ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_aj.R:20:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_aj(...)
5. └─calibmsm:::calib_AJ_boot(...)
6. └─calibmsm (local) calc_aj_subgroup(data_raw_lmk_js$id)
7. └─calibmsm:::calc_aj(...)
8. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
9. │ └─base::withCallingHandlers(...)
10. └─mstate::msfit(csh_aj, trans = tmat)
11. ├─stats::model.matrix(object, data = mf)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_aj.R:68:3'): check calib_pv output, pv_n_pctls specified ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_aj.R:68:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_aj(...)
5. └─calibmsm:::calib_AJ_boot(...)
6. └─base::lapply(transitions_out, apply_calc_aj_subgroup_pctls)
7. └─calibmsm (local) FUN(X[[i]], ...)
8. └─base::lapply(group_ids, calc_aj_subgroup, state_k = state_k)
9. └─calibmsm (local) FUN(X[[i]], ...)
10. └─calibmsm:::calc_aj(...)
11. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
12. │ └─base::withCallingHandlers(...)
13. └─mstate::msfit(csh_aj, trans = tmat)
14. ├─stats::model.matrix(object, data = mf)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:14:3'): check calib_msm output, (j = 1, s = 0), curve_type = rcs, stabilised vs unstabilised ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calib_msm(...) at test-calib_blr.R:14:3
2. └─calibmsm:::calib_blr_ipcw(...)
3. └─calibmsm:::calc_obs_blr_rcs_boot(...)
4. └─calibmsm::calc_weights(...)
5. └─survival::basehaz(cens_model, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:67:3'): check calib_msm output, (j = 1, s = 0), curve_type = loess ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calib_msm(...) at test-calib_blr.R:67:3
2. └─calibmsm:::calib_blr_ipcw(...)
3. └─calibmsm:::calc_obs_blr_loess_boot(...)
4. └─calibmsm::calc_weights(...)
5. └─survival::basehaz(cens_model, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:192:3'): check calib_msm output, (j = 3, s = 100) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_blr.R:192:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_blr_ipcw(...)
5. └─calibmsm:::calc_obs_blr_rcs_boot(...)
6. └─calibmsm::calc_weights(...)
7. └─survival::basehaz(cens_model, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:222:3'): check calib_msm output, (j = 1, s = 0), null covs ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calib_msm(...) at test-calib_blr.R:222:3
2. └─calibmsm:::calib_blr_ipcw(...)
3. └─calibmsm:::calc_obs_blr_rcs_boot(...)
4. └─calibmsm::calc_weights(...)
5. └─survival::basehaz(cens_model, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:371:13'): check calib_msm output, (j = 1, s = 0),
manual weights,
manually define vector of predicted probabilities,
manually define transition out,
estimate curves using rcs ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-calib_blr.R:371:13
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:426:13'): check calib_msm output, (j = 1, s = 0),
manual weights,
manually define vector of predicted probabilities,
manually define transition out,
estimate curves using loess ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-calib_blr.R:426:13
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_blr.R:1008:3'): test warnings and errors ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-calib_blr.R:1008:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_mlr.R:32:3'): check calib_msm output ─────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_mlr.R:32:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_mlr_ipcw(...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, 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-calib_mlr.R:67:3'): check calib_msm output with CI = TRUE (for assess_mean) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_mlr.R:67:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_mlr_ipcw(...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-calib_mlr.R:105:13'): check calib_msm output, (j = 1, s = 0),
Manually define function to estimate weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_mlr.R:105:13
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_mlr_ipcw(...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, 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-calib_pv.R:153:3'): check calib_pv output, (j = 1, s = 0), curve_type = loess, CI_type = parametric ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-calib_pv.R:153:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_pv(...)
5. └─calibmsm:::calc_obs_pv_boot(...)
6. └─calibmsm (local) calc_pv_subgroup(data_raw_lmk_js$id)
7. └─calibmsm:::calc_aj(...)
8. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
9. │ └─base::withCallingHandlers(...)
10. └─mstate::msfit(csh_aj, trans = tmat)
11. ├─stats::model.matrix(object, data = mf)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:7:3'): check plot_calib_msm output (j = 1, s = 0) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calib_msm(...) at test-plot_calib.R:7:3
2. └─calibmsm:::calib_blr_ipcw(...)
3. └─calibmsm:::calc_obs_blr_rcs_boot(...)
4. └─calibmsm::calc_weights(...)
5. └─survival::basehaz(cens_model, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:48:3'): check plot_calib_msm output (j = 1, s = 0) with CI ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calib_msm(...) at test-plot_calib.R:48:3
2. └─calibmsm:::calib_blr_ipcw(...)
3. └─boot::boot(...)
4. └─calibmsm (local) statistic(data, original, ...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, 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-plot_calib.R:86:3'): check plot_calib_msm output (j = 3, s = 100) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:86:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_blr_ipcw(...)
5. └─calibmsm:::calc_obs_blr_rcs_boot(...)
6. └─calibmsm::calc_weights(...)
7. └─survival::basehaz(cens_model, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:122:3'): check plot_calib_pv output (j = 1, s = 0) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:122:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_pv(...)
5. └─calibmsm:::calc_obs_pv_boot(...)
6. └─calibmsm (local) calc_pv_subgroup(data_raw_lmk_js$id)
7. └─calibmsm:::calc_aj(...)
8. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
9. │ └─base::withCallingHandlers(...)
10. └─mstate::msfit(csh_aj, trans = tmat)
11. ├─stats::model.matrix(object, data = mf)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:156:3'): check plot_calib_pv output (j = 1, s = 0) with CI ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:156:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_pv(...)
5. └─calibmsm:::calc_obs_pv_boot(...)
6. └─calibmsm (local) calc_pv_subgroup(data_raw_lmk_js$id)
7. └─calibmsm:::calc_aj(...)
8. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
9. │ └─base::withCallingHandlers(...)
10. └─mstate::msfit(csh_aj, trans = tmat)
11. ├─stats::model.matrix(object, data = mf)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:193:3'): check plot_calib_pv output (j = 3, s = 100) with CI ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:193:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_pv(...)
5. └─calibmsm:::calc_obs_pv_boot(...)
6. └─calibmsm (local) calc_pv_subgroup(data_raw_lmk_js$id)
7. └─calibmsm:::calc_aj(...)
8. ├─base::suppressWarnings(msfit_aj <- mstate::msfit(csh_aj, trans = tmat))
9. │ └─base::withCallingHandlers(...)
10. └─mstate::msfit(csh_aj, trans = tmat)
11. ├─stats::model.matrix(object, data = mf)
12. └─survival:::model.matrix.coxph(object, data = mf)
13. └─stats::delete.response(object$terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test-plot_calib.R:234:3'): check plot_calib_mlr output (j = 1, s = 0) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:234:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_mlr_ipcw(...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, 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-plot_calib.R:262:3'): check plot_calib_mlr output (j = 3, s = 100) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-plot_calib.R:262:3
2. │ └─base::withCallingHandlers(...)
3. └─calibmsm::calib_msm(...)
4. └─calibmsm:::calib_mlr_ipcw(...)
5. └─calibmsm::calc_weights(...)
6. └─survival::basehaz(cens_model, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-weights.R:4:3'): check weights, stabilised == FALSE ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-weights.R:4:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-weights.R:44:3'): check weights, stabilised == TRUE ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-weights.R:44:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-weights.R:85:3'): check weights, stabilised == FALSE, add max_follow ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-weights.R:85:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-weights.R:142:3'): check weights, stabilised == FALSE, covs = null ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-weights.R:142:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-weights.R:181:3'): check weights at j = 1 and s= 100, landmark_type = state/all ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─calibmsm::calc_weights(...) at test-weights.R:181:3
2. └─survival::basehaz(cens_model, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 26 | WARN 0 | SKIP 15 | PASS 14 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc