* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/lillies.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘lillies/DESCRIPTION’ ... OK
* this is package ‘lillies’ version ‘0.2.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lillies’ can be installed ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [11s/11s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [55s/56s] OK
* checking examples with --run-donttest ... [30m/31m] ERROR
Running examples in ‘lillies-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.lyl_ci
> ### Title: Plot evolution of bootstrapped parameters for Life Years Lost
> ### Aliases: plot.lyl_ci
> 
> ### ** Examples
> 
> 
> # Load simulated data as example
> data(simu_data)
> 
> # Estimate remaining life expectancy and Life Years
> # Lost after age 45 years and before age 95 years
> lyl_estimation <- lyl(data = simu_data, t = age_death, status = death,
+                       age_specific = 45, tau = 95)
1. Preparing and checking data...
2. Type of outcome data: 'logical' (TRUE = death / FALSE = alive) [no competing risks - one cause of death]
3. Estimating...
4. Almost there...
Done!
> 
> ## No test: 
> # Calculate bootstrapped confidence interval (10 iterations to test)
> lyl_estimation_ci <- lyl_ci(lyl_estimation, niter = 10)
Bootstrap estimation of confidence intervals [10 iterations]
Done!
> plot(lyl_estimation_ci)
> 
> # Estimate remaining life expectancy and Life Years
> # Lost after each age from 0 to 94 years and before age 95 years
> lyl_estimation2 <- lyl_range(data = simu_data, t = age_death, status = death,
+                              age_begin = 0, age_end = 94, tau = 95)
1. Preparing and checking data...
2. Type of outcome data: 'logical' (TRUE = death / FALSE = alive) [no competing risks - one cause of death]
3. Estimate LYL for ages 0-94 years and numbers at risk for ages 0-95 years...
Done!
> 
> # Calculate bootstrapped confidence interval
> lyl_estimation_ci2 <- lyl_ci(lyl_estimation2)
Bootstrap estimation of confidence intervals [1000 iterations]
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/lillies.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 32:39.55, 1889.92 + 25.32