Last updated on 2026-10-24 01:51:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.0 | 5.53 | 110.52 | 116.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.0 | 4.54 | 52.89 | 57.43 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.9.0 | 86.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.0 | 84.43 | OK | |||
| r-devel-windows-x86_64 | 0.9.0 | 9.00 | 136.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 0.9.0 | 5.77 | 104.88 | 110.65 | OK | |
| r-release-linux-x86_64 | 0.9.0 | 5.84 | 105.36 | 111.20 | OK | |
| r-release-macos-arm64 | 0.9.0 | 2.00 | 40.00 | 42.00 | OK | |
| r-release-macos-x86_64 | 0.9.0 | 5.00 | 143.00 | 148.00 | OK | |
| r-release-windows-x86_64 | 0.9.0 | 8.00 | 135.00 | 143.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.0 | 1.00 | 31.00 | 32.00 | OK | |
| r-oldrel-macos-x86_64 | 0.9.0 | 4.00 | 142.00 | 146.00 | OK | |
| r-oldrel-windows-x86_64 | 0.9.0 | 12.00 | 160.00 | 172.00 | OK |
Version: 0.9.0
Check: examples
Result: ERROR
Running examples in ‘survdt-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Survdt2
> ### Title: Create a survival object for use with time-varying covariates
> ### Aliases: Survdt2 survdt2to1 [.Survdt2 is.na.Survdt2 is.Survdt2
> ### length.Survdt2 as.data.frame.Survdt2 plot.Survdt2
>
> ### ** Examples
>
> # first create (start, stop] data frame;
> # could then apply time transformations
> # to covariates
> splitdat <- time_split(aids, cut = c(20, 40),
+ stop_name = "incu",
+ id_name = "id",
+ origin = -1)
>
> y1 <- with(splitdat,
+ Survdt2(start, incu, event, ltrunc, rtrunc, id))
Warning in x[complete_id_indx, ] :
length of dimension 1 is not a multiple of logical subscript length
> plot(y1)
Ignoring unknown labels:
• colour : ""
>
> y2 <- with(aids,
+ Survdt(incu, ltrunc, rtrunc))
> max(abs(unclass(survdt2to1(y1)) - unclass(y2)))
[1] 0
>
>
> coxph_indtrunc(Survdt2(start, incu, event, ltrunc, rtrunc, id) ~ age_gp,
+ data = splitdat)
Warning in x[complete_id_indx, ] :
length of dimension 1 is not a multiple of logical subscript length
Warning in x[complete_id_indx, ] :
length of dimension 1 is not a multiple of logical subscript length
Error in a$specials[[i]] : subscript out of bounds
Calls: coxph_indtrunc ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cox-regression-quasiindep.Rmd’ using rmarkdown
Quitting from cox-regression-quasiindep.Rmd:45-50 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─survdt::coxph_indtrunc(...)
2. ├─base::t(stats::residuals(cox_fit, "score", weighted = TRUE, collapse = vals$id[vals$sorted_cc]))
3. ├─stats::residuals(cox_fit, "score", weighted = TRUE, collapse = vals$id[vals$sorted_cc])
4. └─survival:::residuals.coxph(...)
5. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
6. ├─stats::model.matrix(fit, data = mf)
7. └─survival:::model.matrix.coxph(fit, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'cox-regression-quasiindep.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘cox-regression-quasiindep.Rmd’
--- re-building ‘nonparametric-analysis.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘nonparametric-analysis.Rmd’
SUMMARY: processing the following file failed:
‘cox-regression-quasiindep.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc