Last updated on 2026-10-24 15:51:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 5.1 | 117.34 | 219.55 | 336.89 | OK | |
| r-devel-linux-x86_64-debian-gcc | 5.1 | 104.54 | 166.08 | 270.62 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 5.1 | 77.00 | 158.05 | 235.05 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 5.1 | 110.00 | 155.74 | 265.74 | OK | |
| r-devel-windows-x86_64 | 5.1 | 122.00 | 471.00 | 593.00 | OK | |
| r-patched-linux-x86_64 | 5.1 | 138.49 | 214.04 | 352.53 | OK | |
| r-release-linux-x86_64 | 5.1 | 131.90 | 212.81 | 344.71 | OK | |
| r-release-macos-arm64 | 5.1 | 29.00 | 50.00 | 79.00 | OK | |
| r-release-macos-x86_64 | 5.1 | 92.00 | 291.00 | 383.00 | OK | |
| r-release-windows-x86_64 | 5.1 | 124.00 | 174645.00 | 174769.00 | FAIL | |
| r-oldrel-macos-arm64 | 5.1 | 31.00 | 67.00 | 98.00 | OK | |
| r-oldrel-macos-x86_64 | 5.1 | 89.00 | 225.00 | 314.00 | OK | |
| r-oldrel-windows-x86_64 | 5.1 | 164.00 | 412.00 | 576.00 | OK |
Version: 5.1
Check: examples
Result: ERROR
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: survfit.coxnet
> ### Title: Compute a survival curve from a coxnet object
> ### Aliases: survfit.coxnet
>
> ### ** Examples
>
> set.seed(2)
> nobs <- 100; nvars <- 15
> xvec <- rnorm(nobs * nvars)
> xvec[sample.int(nobs * nvars, size = 0.4 * nobs * nvars)] <- 0
> x <- matrix(xvec, nrow = nobs)
> beta <- rnorm(nvars / 3)
> fx <- x[, seq(nvars / 3)] %*% beta / 3
> ty <- rexp(nobs, exp(fx))
> tcens <- rbinom(n = nobs, prob = 0.3, size = 1)
> y <- survival::Surv(ty, tcens)
> fit1 <- glmnet(x, y, family = "cox")
Warning: Starting in glmnet 5.1, the default Cox tie-handling method will change from 'breslow' to 'efron' (matching survival::coxph). To silence this message and lock in the v5.0 default, pass cox.ties = 'breslow' explicitly. To preview the v5.1 behavior, pass cox.ties = 'efron'.
>
> # survfit object for Cox model where lambda = 0.1
> sf1 <- survival::survfit(fit1, s = 0.1, x = x, y = y)
Error in a$specials[[i]] : subscript out of bounds
Calls: <Anonymous> ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 5.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
Quitting from Coxnet.Rmd:254-257 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
x
1. +-survival::survfit(fit, s = 0.05, x = x, y = y)
2. \-glmnet:::survfit.coxnet(fit, s = 0.05, x = x, y = y)
3. +-base::do.call(survfit, current_args)
4. +-survival (local) `<fn>`(...)
5. \-survival:::survfit.coxph(...)
6. \-survival:::model.matrix.coxph(object, data = mf)
7. \-stats::delete.response(object$terms)
8. \-stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Coxnet.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘Coxnet.Rmd’
--- re-building ‘coxdev.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘coxdev.Rmd’
--- re-building ‘glmnet-history.Rmd’ using rmarkdown
--- finished re-building ‘glmnet-history.Rmd’
--- re-building ‘glmnet.Rmd’ using rmarkdown
--- finished re-building ‘glmnet.Rmd’
--- re-building ‘glmnetFamily.Rmd’ using rmarkdown
--- finished re-building ‘glmnetFamily.Rmd’
--- re-building ‘relax.Rmd’ using rmarkdown
--- finished re-building ‘relax.Rmd’
SUMMARY: processing the following file failed:
‘Coxnet.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 5.1
Check: re-building of vignette outputs
Result: FAIL
Flavor: r-release-windows-x86_64