Last updated on 2026-10-24 03:56:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.1 | 12.97 | 111.86 | 124.83 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.3.1 | 9.67 | 77.74 | 87.41 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.1 | 11.00 | 96.54 | 107.54 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.3.1 | 9.00 | 79.26 | 88.26 | OK | |
| r-devel-windows-x86_64 | 2.3.1 | 18.00 | 168.00 | 186.00 | OK | |
| r-patched-linux-x86_64 | 2.3.1 | 12.69 | 101.95 | 114.64 | OK | |
| r-release-linux-x86_64 | 2.3.1 | 10.42 | 102.62 | 113.04 | OK | |
| r-release-macos-arm64 | 2.3.1 | 3.00 | 44.00 | 47.00 | OK | |
| r-release-macos-x86_64 | 2.3.1 | 9.00 | 159.00 | 168.00 | OK | |
| r-release-windows-x86_64 | 2.3.1 | 15.00 | 156.00 | 171.00 | OK | |
| r-oldrel-macos-arm64 | 2.3.1 | 5.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 2.3.1 | 9.00 | 131.00 | 140.00 | OK | |
| r-oldrel-windows-x86_64 | 2.3.1 | 19.00 | 196.00 | 215.00 | OK |
Version: 2.3.1
Check: examples
Result: ERROR
Running examples in ‘pencal-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: survplot_prc
> ### Title: Visualize survival predictions for a fitted PRC model
> ### Aliases: survplot_prc
>
> ### ** Examples
>
> # generate example data
> simdata = simulate_prclmm_data(n = 100, p = 4, p.relev = 2,
+ t.values = c(0, 0.2, 0.5, 1, 1.5, 2),
+ landmark = 2, seed = 123)
>
> # estimate the PRC-LMM model
> y.names = paste('marker', 1:4, sep = '')
> step1 = fit_lmms(y.names = y.names,
+ fixefs = ~ age, ranefs = ~ age | id,
+ long.data = simdata$long.data,
+ surv.data = simdata$surv.data,
+ t.from.base = t.from.base,
+ n.boots = 0)
Sorting long.data by subject id
Sorting surv.data by subject id
Preliminary step: remove measurements taken after event / censoring.
Removed: 0 measurements. Retained: 600 measurements.
This computation will be run without parallelization
Estimating the LMMs on the original dataset...
...done
> step2 = summarize_lmms(object = step1)
This computation will be run without parallelization
Computing the predicted random effects on the original dataset...
...done
> step3 = fit_prclmm(object = step2, surv.data = simdata$surv.data,
+ baseline.covs = ~ baseline.age,
+ penalty = 'ridge')
Estimating penalized Cox model on the original dataset...
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'.
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'.
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'.
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'.
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'.
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'.
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'.
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'.
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'.
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'.
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'.
...done
>
> # visualize the predicted survival for subjects 1, 3, 7 and 13
> survplot_prc(step1, step2, step3, ids = c(1, 3, 7, 13), tmax = 6)
Error in a$specials[[i]] : subscript out of bounds
Calls: survplot_prc ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fit_prclmm 0.287 0.014 6.450
summarize_lmms 0.086 0.002 5.751
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.1
Check: package dependencies
Result: ERROR
Package required but not available: ‘survcomp’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64