Last updated on 2026-10-24 09:50:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.2 | 54.00 | 431.68 | 485.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.3.2 | 39.02 | 212.83 | 251.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.2 | 41.00 | 291.82 | 332.82 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.3.2 | 43.00 | 292.79 | 335.79 | OK | |
| r-devel-windows-x86_64 | 2.3.2 | 62.00 | 551.00 | 613.00 | OK | |
| r-patched-linux-x86_64 | 2.3.2 | 58.06 | 403.36 | 461.42 | OK | |
| r-release-linux-x86_64 | 2.3.2 | 55.37 | 405.05 | 460.42 | OK | |
| r-release-macos-arm64 | 2.3.2 | 12.00 | 94.00 | 106.00 | OK | |
| r-release-macos-x86_64 | 2.3.2 | 34.00 | 477.00 | 511.00 | OK | |
| r-release-windows-x86_64 | 2.3.2 | 66.00 | 478.00 | 544.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.2 | OK | ||||
| r-oldrel-macos-x86_64 | 2.3.2 | 30.00 | 387.00 | 417.00 | OK | |
| r-oldrel-windows-x86_64 | 2.3.2 | 83.00 | 599.00 | 682.00 | OK |
Version: 2.3.2
Check: examples
Result: ERROR
Running examples in ‘flexsurv-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flexsurvspline
> ### Title: Flexible survival regression using the Royston/Parmar spline
> ### model.
> ### Aliases: flexsurvspline
> ### Keywords: models survival
>
> ### ** Examples
>
>
> ## Best-fitting model to breast cancer data from Royston and Parmar (2002)
> ## One internal knot (2 df) and cumulative odds scale
>
> spl <- flexsurvspline(Surv(recyrs, censrec) ~ group, data=bc, k=1, scale="odds")
Error in a$specials[[i]] : subscript out of bounds
Calls: flexsurvspline ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.2
Check: tests
Result: ERROR
Running ‘test_base.R’ [54s/74s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
> test_partial <- FALSE
>
> if (test_partial)
+ options(
+ warnPartialMatchArgs = TRUE,
+ warnPartialMatchAttr = TRUE,
+ warnPartialMatchDollar = TRUE
+ )
>
> if (require("testthat")){
+ test_check("flexsurv")
+ }
Loading required package: testthat
Loading required package: flexsurv
Loading required package: survival
Saving _problems/test_fmsm-51.R
Saving _problems/test_mstate-7.R
Saving _problems/test_outputs-40.R
Saving _problems/test_outputs-51.R
Saving _problems/test_predict-386.R
Saving _problems/test_spline-7.R
Saving _problems/test_splinedist-84.R
[ FAIL 7 | WARN 1 | SKIP 4 | PASS 549 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test_standsurv.R:276:3'
• empty test (3): , ,
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_fmsm.R:51:3'): ajfit_fmsm ──────────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(ajfit_fmsm(weim, maxt = 5)$val[1], 1) at test_fmsm.R:51:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─flexsurv::ajfit_fmsm(weim, maxt = 5)
5. └─mstate::msfit(cf, trans = attr(x, "trans"))
6. ├─stats::model.matrix(object, data = mf)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_mstate.R:7:1'): (code run outside of `test_that()`) ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_mstate.R:7:1
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_outputs.R:40:5'): newdata in summary.flexsurvreg: dynamic cut, unknown factor level ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_outputs.R:40:5
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_outputs.R:51:1'): (code run outside of `test_that()`) ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_outputs.R:51:1
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_predict.R:386:3'): predictions with missing data (spline) ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_predict.R:386:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_spline.R:7:1'): (code run outside of `test_that()`) ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_spline.R:7:1
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test_splinedist.R:84:1'): (code run outside of `test_that()`) ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test_splinedist.R:84:1
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
[ FAIL 7 | WARN 1 | SKIP 4 | PASS 549 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘standsurv.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘standsurv.Rmd’
--- re-building ‘flexsurv.Rnw’ using knitr
Quitting from flexsurv.Rnw:929-932 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
x
1. \-flexsurv::flexsurvspline(...)
2. +-base::do.call("flexsurvreg", args)
3. \-flexsurv::flexsurvreg(...)
4. \-dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. +-survival::survfit(cox, newdata = newdata)
6. \-survival:::survfit.coxph(cox, newdata = newdata)
7. \-survival:::model.matrix.coxph(object, data = mf)
8. \-stats::delete.response(object$terms)
9. \-stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'flexsurv.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘flexsurv.Rnw’
--- re-building ‘multistate.Rnw’ using knitr
Quitting from multistate.Rnw:362-366 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
x
1. \-mstate::msfit(crcox, trans = tmat)
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]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'multistate.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘multistate.Rnw’
--- re-building ‘distributions.Rnw’ using Sweave
--- finished re-building ‘distributions.Rnw’
--- re-building ‘flexsurv-examples.Rnw’ using Sweave
Loading required package: survival
Forming integrated rmst function...
Forming integrated mean function...
Loading required package: TH.data
Loading required package: MASS
Attaching package: ‘TH.data’
The following object is masked from ‘package:MASS’:
geyser
Error: processing vignette 'flexsurv-examples.Rnw' failed with diagnostics:
chunk 7
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘flexsurv-examples.Rnw’
SUMMARY: processing the following files failed:
‘flexsurv.Rnw’ ‘multistate.Rnw’ ‘flexsurv-examples.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc