Last updated on 2026-10-24 09:50:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 7.47 | 254.12 | 261.59 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 5.97 | 73.04 | 79.01 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 166.95 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 171.50 | OK | |||
| r-devel-windows-x86_64 | 0.1.0 | 8.00 | 235.00 | 243.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 7.88 | 237.10 | 244.98 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 7.29 | 239.63 | 246.92 | OK | |
| r-release-macos-arm64 | 0.1.0 | 2.00 | 56.00 | 58.00 | OK | |
| r-release-macos-x86_64 | 0.1.0 | 5.00 | 241.00 | 246.00 | OK | |
| r-release-windows-x86_64 | 0.1.0 | 9.00 | 222.00 | 231.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 2.00 | 61.00 | 63.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.0 | 5.00 | 214.00 | 219.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 12.00 | 315.00 | 327.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘clusteredMSM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit_chaz
> ### Title: Fit Cox Model Stratified by Transition and Return Cumulative
> ### Hazards
> ### Aliases: fit_chaz
>
> ### ** Examples
>
> data(example_msm)
> tmat <- trans_mat(list(c(2, 3), c(1, 3), integer(0)),
+ names = c("Healthy", "Ill", "Dead"))
>
> # fit_chaz takes long-format data; intervals_to_long() converts
> # the interval format users supply. Most users reach fit_chaz
> # indirectly via patp() -- this example shows the manual pipeline.
> long <- intervals_to_long(example_msm, tmat)
> haz <- fit_chaz(long, tmat)
Error in a$specials[[i]] : subscript out of bounds
Calls: fit_chaz ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard testthat package layout.
> # It is the entry point used by R CMD check to run all tests under
> # tests/testthat/.
>
> library(testthat)
> library(clusteredMSM)
>
> test_check("clusteredMSM")
Saving _problems/test-fit_chaz-24.R
Saving _problems/test-fit_chaz-35.R
Saving _problems/test-fit_chaz-47.R
Saving _problems/test-fit_chaz-58.R
Saving _problems/test-fit_chaz-67.R
Saving _problems/test-methods-43.R
Saving _problems/test-methods-57.R
Saving _problems/test-methods-65.R
Saving _problems/test-methods-72.R
Saving _problems/test-methods-80.R
Saving _problems/test-methods-99.R
Saving _problems/test-patp-79.R
Saving _problems/test-patp-97.R
Saving _problems/test-patp-113.R
Saving _problems/test-patp-149.R
Saving _problems/test-patp-161.R
Saving _problems/test-patp-173.R
Saving _problems/test-patp-189.R
Saving _problems/test-patp-203.R
Saving _problems/test-patp-217.R
Saving _problems/test-patp-231.R
Saving _problems/test-patp-244.R
Saving _problems/test-patp-259.R
Saving _problems/test-patp-273.R
Saving _problems/test-patp-288.R
Saving _problems/test-patp-393.R
Saving _problems/test-regression-mstate-105.R
[ FAIL 27 | WARN 0 | SKIP 0 | PASS 192 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fit_chaz.R:24:3'): fit_chaz returns expected columns and types ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::fit_chaz(msd, tmat) at test-fit_chaz.R:24:3
2. └─survival::basehaz(fit, 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-fit_chaz.R:35:3'): fit_chaz output is sorted by transition then time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::fit_chaz(msd, tmat) at test-fit_chaz.R:35:3
2. └─survival::basehaz(fit, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_chaz.R:47:3'): fit_chaz cumulative hazards are monotonically non-decreasing ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::fit_chaz(msd, tmat) at test-fit_chaz.R:47:3
2. └─survival::basehaz(fit, 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-fit_chaz.R:58:3'): fit_chaz contains all expected transition IDs ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::fit_chaz(msd, tmat) at test-fit_chaz.R:58:3
2. └─survival::basehaz(fit, centered = FALSE)
3. ├─survival::survfit(fit, se.fit = FALSE)
4. └─survival:::survfit.coxph(fit, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_chaz.R:67:3'): fit_chaz weights argument is honored ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::fit_chaz(msd, tmat) at test-fit_chaz.R:67:3
2. └─survival::basehaz(fit, 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-methods.R:43:3'): print.patp prints expected sections for one-sample fit ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM (local) make_simple_fit() at test-methods.R:43:3
2. └─clusteredMSM::patp(...) at test-methods.R:36:3
3. └─clusteredMSM:::.patp_onesample(...)
4. └─clusteredMSM:::.patp_point(...)
5. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
6. └─survival::basehaz(fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-methods.R:57:3'): print.patp shows test info for two-sample fit ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(make_simple_fit(two_sample = TRUE)) at test-methods.R:57:3
2. │ └─base::withCallingHandlers(...)
3. └─clusteredMSM (local) make_simple_fit(two_sample = TRUE)
4. └─clusteredMSM::patp(...) at test-methods.R:36:3
5. └─clusteredMSM:::.patp_twosample(...)
6. └─clusteredMSM:::.patp_point(...)
7. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
8. └─survival::basehaz(fit, centered = FALSE)
9. ├─survival::survfit(fit, se.fit = FALSE)
10. └─survival:::survfit.coxph(fit, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test-methods.R:65:3'): print.patp signals B = 0 explicitly ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM (local) make_simple_fit(B = 0) at test-methods.R:65:3
2. └─clusteredMSM::patp(...) at test-methods.R:36:3
3. └─clusteredMSM:::.patp_onesample(...)
4. └─clusteredMSM:::.patp_point(...)
5. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
6. └─survival::basehaz(fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-methods.R:72:3'): summary.patp returns a summary.patp object ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM (local) make_simple_fit() at test-methods.R:72:3
2. └─clusteredMSM::patp(...) at test-methods.R:36:3
3. └─clusteredMSM:::.patp_onesample(...)
4. └─clusteredMSM:::.patp_point(...)
5. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
6. └─survival::basehaz(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-methods.R:80:3'): print.summary.patp prints the full curves ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM (local) make_simple_fit() at test-methods.R:80:3
2. └─clusteredMSM::patp(...) at test-methods.R:36:3
3. └─clusteredMSM:::.patp_onesample(...)
4. └─clusteredMSM:::.patp_point(...)
5. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
6. └─survival::basehaz(fit, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test-methods.R:97:3'): print.patp works with no clustering (n_clusters = NA) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-methods.R:97:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:76:3'): patp one-sample formula returns expected structure ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:76:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:94:3'): patp two-sample formula returns test slot ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:94:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:111:3'): patp B = 0 returns point estimate only ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:111:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:147:3'): patp without cluster uses individual-level bootstrap ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:147:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:159:3'): patp probabilities are in [0, 1] ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:159:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:170:3'): patp seed produces reproducible results ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:170:3
2. └─clusteredMSM:::.patp_onesample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:186:3'): patp two-sample detects substantial group differences ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:186:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:199:3'): patp design = 'shared' works on case (i) data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:199:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:213:3'): patp design = 'cluster_random' works on case (ii) data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:213:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:227:3'): patp design = 'indep_random' works on case (ii) data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:227:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, 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-patp.R:241:3'): patp design = 'auto' picks 'shared' on case (i) data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─clusteredMSM::patp(...) at test-patp.R:241:3
2. └─clusteredMSM:::.patp_twosample(...)
3. └─clusteredMSM:::.patp_point(...)
4. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
5. └─survival::basehaz(fit, centered = FALSE)
6. ├─survival::survfit(fit, se.fit = FALSE)
7. └─survival:::survfit.coxph(fit, se.fit = FALSE)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:253:3'): patp design = 'auto' picks 'indep_random' on case (ii) data and warns ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-patp.R:253:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─clusteredMSM::patp(...)
8. └─clusteredMSM:::.patp_twosample(...)
9. └─clusteredMSM:::.patp_point(...)
10. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
11. └─survival::basehaz(fit, centered = FALSE)
12. ├─survival::survfit(fit, se.fit = FALSE)
13. └─survival:::survfit.coxph(fit, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:267:3'): patp design = 'auto' on case (i) does not warn ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-patp.R:267:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─clusteredMSM::patp(...)
8. └─clusteredMSM:::.patp_twosample(...)
9. └─clusteredMSM:::.patp_point(...)
10. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
11. └─survival::basehaz(fit, centered = FALSE)
12. ├─survival::survfit(fit, se.fit = FALSE)
13. └─survival:::survfit.coxph(fit, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:281:3'): patp design = 'indep_random' explicit does not warn ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-patp.R:281:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─clusteredMSM::patp(...)
8. └─clusteredMSM:::.patp_twosample(...)
9. └─clusteredMSM:::.patp_point(...)
10. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
11. └─survival::basehaz(fit, centered = FALSE)
12. ├─survival::survfit(fit, se.fit = FALSE)
13. └─survival:::survfit.coxph(fit, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test-patp.R:388:3'): patp runs with cband = TRUE and produces band columns ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-patp.R:388:3
2. │ └─base::withCallingHandlers(...)
3. └─clusteredMSM::patp(...)
4. └─clusteredMSM:::.patp_onesample(...)
5. └─clusteredMSM:::.patp_point(...)
6. └─clusteredMSM::fit_chaz(data, tmat, weights = w)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test-regression-mstate.R:105:3'): prodint_AJ agrees with mstate::probtrans on a progressive model ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─mstate::msfit(cox_m, trans = tmat_m, variance = FALSE) at test-regression-mstate.R:105:3
2. ├─stats::model.matrix(object, data = mf)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
[ FAIL 27 | WARN 0 | SKIP 0 | PASS 192 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc