Last updated on 2026-10-24 12:51:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.0 | 13.72 | 132.75 | 146.47 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.0 | 9.29 | 72.59 | 81.88 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.0 | 9.00 | 87.15 | 96.15 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.7.0 | 99.28 | OK | |||
| r-devel-windows-x86_64 | 0.7.0 | 16.00 | 139.00 | 155.00 | OK | |
| r-patched-linux-x86_64 | 0.7.0 | 11.87 | 122.34 | 134.21 | OK | |
| r-release-linux-x86_64 | 0.7.0 | 13.57 | 123.60 | 137.17 | OK | |
| r-release-macos-arm64 | 0.7.0 | 3.00 | 34.00 | 37.00 | OK | |
| r-release-macos-x86_64 | 0.7.0 | 9.00 | 194.00 | 203.00 | OK | |
| r-release-windows-x86_64 | 0.7.0 | 17.00 | 131.00 | 148.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.7.0 | 8.00 | 123.00 | 131.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.0 | 19.00 | 176.00 | 195.00 | OK |
Version: 0.7.0
Check: examples
Result: ERROR
Running examples in ‘blapsr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coxlps
> ### Title: Fit a Cox proportional hazards regression model with
> ### Laplace-P-splines.
> ### Aliases: coxlps
>
> ### ** Examples
>
>
> ### Example 1 (Simulated survival data)
>
> set.seed(3)
>
> # Simulate survival data with simsurvdata
> betas <- c(0.13, 0.52, 0.30)
> simul <- simsurvdata(a = 3.8, b = 2.2, n = 250, betas = betas , censperc = 20)
> simul
Sample size: 250
Censoring: Exponential
Number of events: 199
Censoring percentage: 20.4%
Weibull mean: 1.99
Weibull variance: 0.34
> simdat <- simul$survdata
> plot(simul) # Plot survival data
>
> # Estimation with coxlps
> fit <- coxlps(Surv(time, delta) ~ x1 + x2 + x3, data = simdat, K = 15)
> # Compare coxlps and coxph
> fit
Formula:
Surv(time, delta) ~ x1 + x2 + x3
Object class: "coxlps"
Number of B-splines in basis: 15
Number of parametric coeffs.: 3
Latent vector dimension : 18
Penalty order : 2
Sample size : 250
Number of events: : 199
Effective dimension (ED) : 5.01
Estimated model coefficients:
coef exp(coef) sd.post z
x1 0.2167 1.2419 0.0697 3.1072
x2 0.4787 1.6140 0.0800 5.9818
x3 0.2023 1.2242 0.0831 2.4332
exp(coef) exp(-coef) lower.95 upper.95
x1 1.2419 0.8052 1.0830 1.4226
x2 1.6140 0.6196 1.3775 1.8863
x3 1.2242 0.8169 1.0384 1.4394
---
AIC.p = 468.5794 AIC.ED = 472.5963
BIC.p = 478.4593 BIC.ED = 489.0905
> summary(coxph(Surv(time, delta) ~ x1 + x2 + x3, data = simdat))
Call:
coxph(formula = Surv(time, delta) ~ x1 + x2 + x3, data = simdat)
n= 250, number of events= 199
coef exp(coef) se(coef) z Pr(>|z|)
x1 0.20775 1.23091 0.06919 3.003 0.00268 **
x2 0.47557 1.60894 0.08002 5.943 2.8e-09 ***
x3 0.18178 1.19936 0.08272 2.198 0.02798 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
x1 1.231 0.8124 1.075 1.410
x2 1.609 0.6215 1.375 1.882
x3 1.199 0.8338 1.020 1.410
Concordance= 0.637 (se = 0.023 )
Likelihood ratio test= 45.5 on 3 df, p=7e-10
Wald test = 45.8 on 3 df, p=6e-10
Score (logrank) test = 45.95 on 3 df, p=6e-10
>
> # Fitted baseline survival vs target
> plot(fit, h0 = FALSE, cred.int = 0.95, overlay.km = TRUE)
Error in a$specials[[i]] : subscript out of bounds
Calls: plot ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
amlps 3.75 0.055 5.281
Flavor: r-devel-linux-x86_64-debian-gcc