biospear

Running examples in ‘biospear-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expSurv
> ### Title: Computation of expected survival based on a prediction model
> ### Aliases: expSurv predict.resexpSurv plot.resexpSurv
> ### Keywords: survival estimations confidence intervals
> 
> ### ** Examples
> 
> ########################################
> # Simulated data set
> ########################################
> 
> ## Low calculation time
>   set.seed(654321)
>   sdata <- simdata(
+     n = 500, p = 20, q.main = 3, q.inter = 0,
+     prob.tt = 0.5, alpha.tt = 0,
+     beta.main = -0.8,
+     b.corr = 0.6, b.corr.by = 4,
+     m0 = 5, wei.shape = 1, recr = 4, fu = 2,
+     timefactor = 1)
> 
>   resBM <- BMsel(
+     data = sdata, 
+     method = c("lasso", "lasso-pcvl"), 
+     inter = FALSE, 
+     folds = 5)

Computing selection with method: lasso
Warning: Starting in glmnet 5.1, the default Cox tie-handling method wil
...[truncated]...

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'.

Computing selection with method: lasso-pcvl (lasso penalized extensions)
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'.
>   
>   esurv <- expSurv(
+     res = resBM,
+     traindata = sdata,
+     boot = FALSE,
+     time = 5,
+     trace = TRUE)

Computation of the expected survival

Computation of analytical confidence intervals
Error in a$specials[[i]] : subscript out of bounds
Calls: expSurv ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted

Maintainer: ‘Stefan Michiels <stefan.michiels@gustaveroussy.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Nils",
                      family = "Ternes",
                      role = "aut"),
               person(given = "Federico",
                      family = "Rotolo",
                      role = "aut"),
               person(given = "Stefan",
                      family = "Michiels",
                      role = c("aut", "cre"),
                      email = "stefan.michiels@gustaveroussy.fr"))
as necessary.