Last updated on 2026-10-24 09:50:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.3 | 12.70 | 164.67 | 177.37 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 10.23 | 84.94 | 95.17 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.3 | 12.00 | 137.26 | 149.26 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.3 | 119.99 | OK | |||
| r-devel-windows-x86_64 | 0.3.3 | 19.00 | 246.00 | 265.00 | OK | |
| r-patched-linux-x86_64 | 0.3.3 | 14.06 | 144.20 | 158.26 | OK | |
| r-release-linux-x86_64 | 0.3.3 | 13.87 | 145.43 | 159.30 | OK | |
| r-release-macos-arm64 | 0.3.3 | 4.00 | 39.00 | 43.00 | OK | |
| r-release-macos-x86_64 | 0.3.3 | 11.00 | 200.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 0.3.3 | 18.00 | 177.00 | 195.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.3 | OK | ||||
| r-oldrel-macos-x86_64 | 0.3.3 | 11.00 | 162.00 | 173.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.3 | 24.00 | 219.00 | 243.00 | OK |
Version: 0.3.3
Check: Rd contents
Result: NOTE
Rd files without \usage:
‘transhelp.Rd’
\arguments should not be documented without \usage.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.3.3
Check: examples
Result: ERROR
Running examples in ‘mstate-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ELOS
> ### Title: Expected length of stay
> ### Aliases: ELOS
> ### Keywords: univar
>
> ### ** Examples
>
>
> # transition matrix for illness-death model
> tmat <- trans.illdeath()
> # data in wide format, for transition 1 this is dataset E1 of
> # Therneau & Grambsch (2000)
> tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1),
+ dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1),
+ x1=c(1,1,1,0,0,0),x2=c(6:1))
> # data in long format using msprep
> tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"),
+ data=tg,keep=c("x1","x2"),trans=tmat)
> # events
> events(tglong)
$Frequencies
to
from healthy illness death no event total entering
healthy 0 4 2 0 6
illness 0 0 4 0 4
death 0 0 0 6 6
$Proportions
to
from healthy illness death no event
healthy 0.0000000 0.6666667 0.3333333 0.0000000
illness 0.0000000 0.0000000 1.0000000 0.0000000
death 0.0000000 0.0000000 0.0000000 1.0000000
> table(tglong$status,tglong$to,tglong$from)
, , = 1
2 3
0 2 4
1 4 2
, , = 2
2 3
0 0 0
1 0 4
> # expanded covariates
> tglong <- expand.covs(tglong,c("x1","x2"))
> # Cox model with different covariate
> cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans),
+ data=tglong,method="breslow")
> summary(cx)
Call:
coxph(formula = Surv(Tstart, Tstop, status) ~ x1.1 + x2.2 + strata(trans),
data = tglong, method = "breslow")
n= 16, number of events= 10
coef exp(coef) se(coef) z Pr(>|z|)
x1.1 1.4753 4.3723 1.2557 1.175 0.240
x2.2 0.8571 2.3563 0.8848 0.969 0.333
exp(coef) exp(-coef) lower .95 upper .95
x1.1 4.372 0.2287 0.3731 51.24
x2.2 2.356 0.4244 0.4160 13.35
Concordance= 0.781 (se = 0.077 )
Likelihood ratio test= 2.93 on 2 df, p=0.2
Wald test = 2.32 on 2 df, p=0.3
Score (logrank) test = 2.86 on 2 df, p=0.2
> # new data, to check whether results are the same for transition 1 as
> # those in appendix E.1 of Therneau & Grambsch (2000)
> newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3)
> HvH <- msfit(cx,newdata,trans=tmat)
Error in a$specials[[i]] : subscript out of bounds
Calls: msfit ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘visuals_demo.Rmd’ using rmarkdown
Quitting from visuals_demo.Rmd:75-90 [msfit_prep]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─mstate::msfit(object = c1, newdata = WW, 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 'visuals_demo.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘visuals_demo.Rmd’
--- re-building ‘Tutorial.Rnw’ using Sweave
Loading required package: survival
Error: processing vignette 'Tutorial.Rnw' failed with diagnostics:
chunk 18 (label = coxzph)
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘Tutorial.Rnw’
SUMMARY: processing the following files failed:
‘visuals_demo.Rmd’ ‘Tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc