* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ExtendedABSurvTDC.Rcheck’
* using R Under development (unstable) (2025-08-27 r88724)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘ExtendedABSurvTDC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExtendedABSurvTDC’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Dr. Himadri Ghosh <hghosh@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  Moeschberger (12:859)
* checking package namespace information ... OK
* checking package dependencies ... OK
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* checking if there is a namespace ... OK
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* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ExtendedABSurvTDC’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
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* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘ExtendedABSurvTDC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExtendedCoxPred
> ### Title: ExtendedABCoxPH Prediction
> ### Aliases: ExtendedCoxPred
> 
> ### ** Examples
> 
> library("ExtendedABSurvTDC")
> load(system.file("extdata", "data.RData", package = "ExtendedABSurvTDC"))
> PropData<-DataPrep(data =as.data.frame(data_test))
No time interval specified, defaulting to 90 days
Max no. of lactations to be considered not specified. Defaulting to the max no. present among all animals in data
> model<-ExtendedABSurvTDC(PropData)
CoxPH model considering all lactations available in wide data

Warning in agreg.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  10,13,14 ; beta may be infinite. 
> Lact_1<-c("Yes","Yes","Yes","No","No","No","No","No","No","No","No")
> Lact_2<-c("No","No","No","No","Yes","Yes","No","No","No","No","No")
> Lact_3<-c("No","No","No","No","No","No","No","No","Yes","Yes","Yes")
> Lact_4<-c("No","No","No","No","No","No","No","No","No","No","No")
> Lact_5<-c("No","No","No","No","No","No","No","No","No","No","No")
> Lact_6<-c("No","No","No","No","No","No","No","No","No","No","No")
> Lact_7<-c("No","No","No","No","No","No","No","No","No","No","No")
> Lact_8<-c("No","No","No","No","No","No","No","No","No","No","No")
> Lact_9<-c("No","No","No","No","No","No","No","No","No","No","No")
> ndata<- data.frame(Lact_1,Lact_2,Lact_3,Lact_4,Lact_5,Lact_6,Lact_7,
+                    Lact_8,Lact_9)
> NewData<-ndata
> HYS<-2033
> AFC <- 1400
> Y=as.factor(1)
> S=as.factor(1)
> H=as.factor(1)
> NewData_default <- data.frame(AFC, Y, S, NewData) # Data for default argument of "factors"
> ExtendedCoxPred(Model=model, NewData=NewData_default)
Error in UseMethod("survfit") : 
  no applicable method for 'survfit' applied to an object of class "list"
Calls: ExtendedCoxPred -> survfit
Execution halted
* checking PDF version of manual ... [3s/3s] OK
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* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE