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

> ### Name: PEP-class
> ### Title: Penalized Ensemble Predictor (PEP) S4-class ensemble consisting
> ###   of individual PSP-members
> ### Aliases: PEP-class
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # The PEP-construction is wrapped in NOT RUN, because cross-validating multiple PSPs
> ##D # is very time consuming especially if a tight grid of alpha/lambda is to be explored.
> ##D # The simulated data from Turku University Hospital (TYKS) is used as an example:
> ##D data(TYKSSIMU)
> ##D 
> ##D # Two cohorts and corresponding data matrices:
> ##D head(xMEDISIMU)
> ##D head(xTEXTSIMU)
> ##D # Two survival responses:
> ##D head(yMEDISIMU)
> ##D head(xTEXTSIMU)
> ##D 
> ##D # Search L1/L2 norm alpha-grid with 10 values between [0,1]
> ##D aseq <- seq(from=0, to=1, by=0.1)
> ##D # Lambda sequence penalization is of 100 length conditional for each alpha
> ##D nlamb <- 100
> ##D 
> ##D library(survival)
> ##D # Create three ensemble members; one for MEDI cohort, one for TEXT cohort,
> ##D # and finally one member that combines both cohorts simultaneously in a coxnet
> ##D psp1 <- new("PSP", x = rbind(xMEDISIMU, xTEXTSIMU), 
> ##D y = Surv(rbind(yMEDISIMU, yTEXTSIMU)[,"surv"]),
> ##D plot = TRUE, alphaseq = aseq, scorefunc = score.cindex, seed = 1,
> ##D folds = 10, nlambda = nlamb)
> ##D psp2 <- new("PSP", x = xMEDISIMU, 
> ##D y = Surv(yMEDISIMU[,"surv"]),
> ##D plot = TRUE, alphaseq = aseq, scorefunc = score.cindex, seed = 1,
> ##D folds = 10, nlambda = nlamb)
> ##D psp3 <- new("PSP", x = xTEXTSIMU, 
> ##D 	y = Surv(yTEXTSIMU[,"surv"]),
> ##D plot = TRUE, alphaseq = aseq, scorefunc = score.cindex, seed = 1,
> ##D folds = 10, nlambda = nlamb)
> ##D par(mfrow=c(1,3))
> ##D plot(psp1); plot(psp2); plot(psp3); # Inspect the alpha/lambda surfaces
> ##D 
> ##D # Create an ensemble of the above 3 members
> ##D simuens <- new("PEP", PSPs = list(psp1, psp2, psp3))
> ##D simuens
> ##D # Ready PEP-object can be used for novel predictions etc
> ##D 
> ## End(Not run)
> 
> # Run example predictions from a previously optimized PEP-model
> data(ePCRmodels)
> data(TYKSSIMU)
> 
> # Perform risk predictions from the joint cohort ensemble member as an example
> MEDIpred <- predict(TYKS@PSPs[[1]]@fit, s=TYKS@PSPs[[1]]@optimum["Lambda"], 
+ newx = conforminput(TYKS@PSPs[[1]], xMEDISIMU))[,1]
Error: 'predict.coxnet' is not an exported object from 'namespace:glmnet'
Execution halted