Last updated on 2026-10-24 01:51:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 4.75 | 96.90 | 101.65 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 3.29 | 59.82 | 63.11 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 81.16 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 71.47 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 9.00 | 111.00 | 120.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 4.16 | 89.53 | 93.69 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 4.00 | 89.69 | 93.69 | OK | |
| r-release-macos-arm64 | 0.2.0 | 1.00 | 28.00 | 29.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 3.00 | 110.00 | 113.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 7.00 | 104.00 | 111.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.0 | 3.00 | 95.00 | 98.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 8.00 | 132.00 | 140.00 | OK |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘plsmselect-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumbasehaz
> ### Title: Cumulative Baseline Hazard of a gamlasso object
> ### Aliases: cumbasehaz
>
> ### ** Examples
>
> library(plsmselect)
>
> data(simData)
>
> ## Fit Cox gamlasso model using the formula approach:
> ## (L1-penalty both on X terms and smooth terms (bs="ts"))
> simData$X = model.matrix(~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10, data=simData)[,-1]
>
> cfit = gamlasso(time ~ X +
+ s(z1, bs="ts", k=5) +
+ s(z2, bs="ts", k=5) +
+ s(z3, bs="ts", k=5) +
+ s(z4, bs="ts", k=5),
+ data = simData,
+ family = "cox",
+ weights="status",
+ seed=1)
Fitting a lasso and gam loop ...
Warning in .resolve_control(control = control, nvars = nvars, deprecated = list(thresh = if (!missing(thresh)) thresh, :
Passing 'maxit' to glmnet() is deprecated. Use control = list(maxit = ...) instead.
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: from glmnet C++ code (error code -39); Convergence for 39th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -26); Convergence for 26th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -29); Convergence for 29th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -34); Convergence for 34th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -31); Convergence for 31th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -39); Convergence for 39th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -29); Convergence for 29th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -36); Convergence for 36th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -32); Convergence for 32th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -26); Convergence for 26th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -29); Convergence for 29th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -36); Convergence for 36th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -32); Convergence for 32th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -26); Convergence for 26th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -29); Convergence for 29th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -36); Convergence for 36th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -32); Convergence for 32th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -26); Convergence for 26th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -29); Convergence for 29th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -36); Convergence for 36th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -27); Convergence for 27th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -41); Convergence for 41th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -32); Convergence for 32th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
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: from glmnet C++ code (error code -40); Convergence for 40th lambda value not reached after maxit=1000 iterations; solutions for larger lambdas returned
>
> ## Obtain and plot predicted cumulative baseline hazard:
> H0.pred <- cumbasehaz(cfit)
Error in a$specials[[i]] : subscript out of bounds
Calls: cumbasehaz ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘plsmselect.Rmd’ using rmarkdown
Quitting from plsmselect.Rmd:412-419 [coxdiagnos]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─plsmselect::cumbasehaz(cfit)
2. └─plsmselect:::cbh(lp, event.time, status)
3. ├─survival::survfit(cox.model)
4. └─survival:::survfit.coxph(cox.model)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'plsmselect.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘plsmselect.Rmd’
SUMMARY: processing the following file failed:
‘plsmselect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc