Last updated on 2026-10-24 09:51:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 10.85 | 114.52 | 125.37 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 7.45 | 68.48 | 75.93 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 10.00 | 102.80 | 112.80 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 84.56 | NOTE | |||
| r-devel-windows-x86_64 | 1.0.0 | 12.00 | 118.00 | 130.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.0 | 10.59 | 102.61 | 113.20 | NOTE | |
| r-release-linux-x86_64 | 1.0.0 | 10.55 | 101.84 | 112.39 | NOTE | |
| r-release-macos-arm64 | 1.0.0 | 3.00 | 30.00 | 33.00 | NOTE | |
| r-release-macos-x86_64 | 1.0.0 | 7.00 | 130.00 | 137.00 | NOTE | |
| r-release-windows-x86_64 | 1.0.0 | 11.00 | 109.00 | 120.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.0.0 | 7.00 | 105.00 | 112.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.0.0 | 15.00 | 139.00 | 154.00 | NOTE |
Version: 1.0.0
Check: Rd files
Result: NOTE
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘recurrentpseudo-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pseudo.geefit
> ### Title: Function that makes GEE model fit for recurrent
> ### pseudo-observations
> ### Aliases: pseudo.geefit
> ### Keywords: recurrentpseudo
>
> ### ** Examples
>
> # Bladder cancer data from survival package
> require(survival)
Loading required package: survival
>
> # Make a three level status variable
> bladder1$status3 <- ifelse(bladder1$status %in% c(2, 3), 2, bladder1$status)
>
> # Add one extra day for the two patients with start=stop=0
> # subset(bladder1, stop <= start)
> bladder1[bladder1$id == 1, "stop"] <- 1
> bladder1[bladder1$id == 49, "stop"] <- 1
>
> # Restrict the data to placebo and thiotepa
> bladdersub <- subset(bladder1, treatment %in% c("placebo", "thiotepa"))
>
> # Make treatment variable two-level factor
> bladdersub$Z <- as.factor(ifelse(bladdersub$treatment == "placebo", 0, 1))
> levels(bladdersub$Z) <- c("placebo", "thiotepa")
>
> head(bladdersub)
id treatment number size recur start stop status rtumor rsize enum status3
1 1 placebo 1 1 0 0 1 3 . . 1 2
2 2 placebo 1 3 0 0 1 3 . . 1 2
3 3 placebo 2 1 0 0 4 0 . . 1 0
4 4 placebo 1 1 0 0 7 0 . . 1 0
5 5 placebo 5 1 0 0 10 3 . . 1 2
6 6 placebo 4 1 1 0 6 1 1 1 1 1
Z
1 placebo
2 placebo
3 placebo
4 placebo
5 placebo
6 placebo
>
> # Two-dimensional (bivariate pseudo-obs) model fit
>
> # Computation of pseudo-observations
> pseudo_bladder_2d <- pseudo.twodim(tstart = bladdersub$start,
+ tstop = bladdersub$stop,
+ status = bladdersub$status3,
+ id = bladdersub$id,
+ covar_names = "Z",
+ tk = c(30),
+ data = bladdersub)
Error in a$specials[[i]] : subscript out of bounds
Calls: pseudo.twodim ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘recurrentpseudo.Rmd’ using rmarkdown
Quitting from recurrentpseudo.Rmd:196-227 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─recurrentpseudo::pseudo.onedim(...)
2. └─recurrentpseudo:::pseudo.surv_mu_est(...)
3. └─survival::basehaz(...)
4. ├─survival::survfit(fit, se.fit = FALSE)
5. └─survival:::survfit.coxph(fit, 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: processing vignette 'recurrentpseudo.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘recurrentpseudo.Rmd’
SUMMARY: processing the following file failed:
‘recurrentpseudo.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc