Last updated on 2026-10-24 12:51:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.1 | 218.24 | 173.15 | 391.39 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.7.1 | 163.55 | 109.17 | 272.72 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.7.1 | 147.00 | 147.37 | 294.37 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.7.1 | 179.00 | 120.76 | 299.76 | OK | |
| r-devel-windows-x86_64 | 1.7.1 | 237.00 | 318.00 | 555.00 | OK | |
| r-patched-linux-x86_64 | 1.7.1 | 219.69 | 162.33 | 382.02 | OK | |
| r-release-linux-x86_64 | 1.7.1 | 219.55 | 162.03 | 381.58 | OK | |
| r-release-macos-arm64 | 1.7.1 | 48.00 | 16.00 | 64.00 | OK | |
| r-release-macos-x86_64 | 1.7.1 | 147.00 | 194.00 | 341.00 | OK | |
| r-release-windows-x86_64 | 1.7.1 | 237.00 | 247.00 | 484.00 | OK | |
| r-oldrel-macos-arm64 | 1.7.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.7.1 | 147.00 | 170.00 | 317.00 | OK | |
| r-oldrel-windows-x86_64 | 1.7.1 | 293.00 | 294.00 | 587.00 | OK |
Version: 1.7.1
Check: examples
Result: ERROR
Running examples in ‘rstpm2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aft
> ### Title: Parametric accelerated failure time model with smooth time
> ### functions
> ### Aliases: aft
> ### Keywords: survival smooth
>
> ### ** Examples
>
> summary(aft(Surv(rectime,censrec==1)~hormon,data=brcancer,df=4))
Error in (function (cond) :
error in evaluating the argument 'object' in selecting a method for function 'summary': subscript out of bounds
Calls: summary ... model.matrix.coxph -> delete.response -> off -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rstpm2)
Loading required package: survival
Loading required package: splines
Attaching package: 'rstpm2'
The following object is masked from 'package:survival':
colon
>
> test_check("rstpm2")
Saving _problems/test_base-14.R
Saving _problems/test_base-28.R
Saving _problems/test_base-33.R
Saving _problems/test_base-38.R
Saving _problems/test_base-50.R
Saving _problems/test_base-105.R
Saving _problems/test_base-114.R
Saving _problems/test_base-118.R
Saving _problems/test_base-134.R
Saving _problems/test_base-148.R
Saving _problems/test_delayed-14.R
Saving _problems/test_delayed-20.R
Saving _problems/test_delayed-25.R
Saving _problems/test_delayed-36.R
Saving _problems/test_missing-20.R
Saving _problems/test_missing-29.R
Saving _problems/test_missing-37.R
Saving _problems/test_missing-45.R
Saving _problems/test_missing-53.R
Saving _problems/test_missing-73.R
Saving _problems/test_missing-99.R
Saving _problems/test_missing-111.R
Saving _problems/test_missing-123.R
Saving _problems/test_missing-134.R
Saving _problems/test_missing-144.R
Saving _problems/test_missing-154.R
Saving _problems/test_missing-163.R
Saving _problems/test_missing-180.R
Saving _problems/test_missing-200.R
Saving _problems/test_missing-209.R
Saving _problems/test_missing-218.R
Saving _problems/test_missing-226.R
[ FAIL 32 | WARN 0 | SKIP 2 | PASS 25 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_base.R:19:5', 'test_base.R:42:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_base.R:14:5'): base ────────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer) at test_base.R:14:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:27:5'): NelderMead ──────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_base.R:27:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_base.R:33:5'): tvc ─────────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_base.R:33:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:37:5'): Comparison with Stata ───────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_base.R:37:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_base.R:50:5'): probit ──────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_base.R:50:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ ├─stats::qnorm(as.vector(S))
7. │ └─base::as.vector(S)
8. ├─base::pmin(...)
9. ├─base::pmax(...)
10. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
11. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
12. │ └─base::withCallingHandlers(...)
13. ├─survival::survfit(obj, se.fit = FALSE)
14. └─survival:::survfit.coxph(obj, se.fit = FALSE)
15. └─survival:::model.matrix.coxph(object, data = mf)
16. └─stats::delete.response(object$terms)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:105:5'): base ───────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::aft(Surv(rectime, censrec == 1) ~ hormon, data = brcancer) at test_base.R:105:5
2. ├─base::pmax(-18, log(-log(S0hat(coxph.obj))))
3. └─rstpm2:::S0hat(coxph.obj)
4. ├─survival::survfit(obj, se.fit = FALSE)
5. └─survival:::survfit.coxph(obj, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:114:5'): tvc ────────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_base.R:114:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::aft(...)
7. ├─base::pmax(-18, log(-log(S0hat(coxph.obj))))
8. └─rstpm2:::S0hat(coxph.obj)
9. ├─survival::survfit(obj, se.fit = FALSE)
10. └─survival:::survfit.coxph(obj, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:118:5'): Cure ───────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::aft(...)
2. ├─base::pmax(-18, log(-log(S0hat(coxph.obj))))
3. └─rstpm2:::S0hat(coxph.obj)
4. ├─survival::survfit(obj, se.fit = FALSE)
5. └─survival:::survfit.coxph(obj, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:134:5'): base ───────────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(Surv(y, e) ~ x + cluster(id), data = d) at test_base.R:134:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_base.R:148:3'): providing initial values with frailty works ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::gsm(Surv(y, event) ~ 1, dat, df = 1, cluster = dat$grp) at test_base.R:148:3
2. ├─link$link(...)
3. │ └─base::as.vector(S)
4. ├─base::pmin(...)
5. ├─base::pmax(...)
6. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
7. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
8. │ └─base::withCallingHandlers(...)
9. ├─survival::survfit(obj, se.fit = FALSE)
10. └─survival:::survfit.coxph(obj, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_delayed.R:13:5'): Basic test ───────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_delayed.R:13:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_delayed.R:19:5'): Comparison with Stata ────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_delayed.R:19:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_delayed.R:25:5'): pstpm2 ───────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::pstpm2(...) at test_delayed.R:25:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_delayed.R:36:5'): All values zero or one ───────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::aft(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2) at test_delayed.R:36:5
2. ├─base::pmax(-18, log(-log(S0hat(coxph.obj))))
3. └─rstpm2:::S0hat(coxph.obj)
4. ├─survival::survfit(obj, se.fit = FALSE)
5. └─survival:::survfit.coxph(obj, se.fit = FALSE)
6. └─survival:::model.matrix.coxph(object, data = mf)
7. └─stats::delete.response(object$terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:19:5'): Missing event time - stpm2 ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:19:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:28:5'): Invalid event time - stpm2 ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:28:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:37:5'): Missing covariate - stpm2 ────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2) at test_missing.R:37:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_missing.R:45:5'): Missing weight - stpm2 ───────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:45:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:53:5'): Predictions with missing values - stpm2 ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:53:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_missing.R:73:5'): Missing bhazard - stpm2 ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(Surv(y, e) ~ x + bhazard(bg), data = d) at test_missing.R:73:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:97:5'): Missing event time - stpm2+frailty(vector) ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:97:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(...)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:109:5'): Missing event time - stpm2+frailty(character) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:109:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(...)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:121:5'): Missing event time - stpm2+frailty(special) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:121:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(...)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:132:5'): Invalid event time - stpm2+frailty ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:132:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::stpm2(...)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:143:5'): Missing covariate - stpm2+frailty ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:143:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_missing.R:153:5'): Missing weight - stpm2+frailty ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:153:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:162:5'): Missing cluster - stpm2+frailty ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:162:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_missing.R:179:5'): Predictions with missing values - stpm2+frailty ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::stpm2(...) at test_missing.R:179:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:200:5'): Missing event time - pstpm2 ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:200:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::pstpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:209:5'): Invalid event time - pstpm2 ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test_missing.R:209:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─rstpm2::pstpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test_missing.R:218:5'): Missing covariate - pstpm2 ──────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::pstpm2(Surv(rectime, censrec == 1) ~ hormon, data = brcancer2) at test_missing.R:218:5
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, 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_missing.R:226:1'): (code run outside of `test_that()`) ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─rstpm2::pstpm2(...) at test_missing.R:226:1
2. └─base::eval(m, data, parent.frame())
3. └─base::eval(m, data, parent.frame())
4. └─rstpm2::gsm(...)
5. ├─link$link(...)
6. │ └─base::as.vector(S)
7. ├─base::pmin(...)
8. ├─base::pmax(...)
9. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
10. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
11. │ └─base::withCallingHandlers(...)
12. ├─survival::survfit(obj, se.fit = FALSE)
13. └─survival:::survfit.coxph(obj, se.fit = FALSE)
14. └─survival:::model.matrix.coxph(object, data = mf)
15. └─stats::delete.response(object$terms)
16. └─stats (local) off(a$specials[[i]])
[ FAIL 32 | WARN 0 | SKIP 2 | PASS 25 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.7.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction.Rnw’ using Sweave
Loading required package: survival
Loading required package: splines
Attaching package: ‘rstpm2’
The following object is masked from ‘package:survival’:
colon
Error: processing vignette 'Introduction.Rnw' failed with diagnostics:
chunk 2
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘Introduction.Rnw’
--- re-building ‘SimpleGuide.Rnw’ using Sweave
Loading required package: splines
Attaching package: ‘rstpm2’
The following object is masked from ‘package:survival’:
colon
Error: processing vignette 'SimpleGuide.Rnw' failed with diagnostics:
chunk 3
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘SimpleGuide.Rnw’
--- re-building ‘multistate.Rnw’ using Sweave
--- finished re-building ‘multistate.Rnw’
--- re-building ‘predictnl.Rnw’ using Sweave
Loading required package: survival
Loading required package: splines
Attaching package: ‘rstpm2’
The following object is masked from ‘package:survival’:
colon
Error: processing vignette 'predictnl.Rnw' failed with diagnostics:
chunk 7
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘predictnl.Rnw’
SUMMARY: processing the following files failed:
‘Introduction.Rnw’ ‘SimpleGuide.Rnw’ ‘predictnl.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc