* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/GPTCM.Rcheck’
* using R Under development (unstable) (2025-12-22 r89217)
* 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 ‘GPTCM/DESCRIPTION’ ... OK
* this is package ‘GPTCM’ version ‘1.1.3’
* 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 ‘GPTCM’ can be installed ... [75s/76s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking C++ specification ... OK
* checking package directory ... OK
* checking ‘build’ 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 whether startup messages can be suppressed ... 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 ... [18s/18s] 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/61s] OK
* checking examples with --run-donttest ... [37s/35s] ERROR
Running examples in ‘GPTCM-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotBrier
> ### Title: Plot curves of time-dependent Brier score
> ### Aliases: plotBrier
> 
> ### ** Examples
> 
> 
> # simulate data
> set.seed(123)
> n <- 200 # subjects
> p <- 10 # variable selection predictors
> L <- 3 # cell types
> dat <- simData(n, p, L)
> 
> # run a Bayesian GPTCM model: GPTCM-Ber2
> fit <- GPTCM(dat, nIter = 5, burnin = 0)
Running MCMC iterations ...

[##########----------------------------------------] 20%

[##################################################] 100%
> 
> ## No test: 
> plotBrier(dat, datMCMC = fit, PTCM = FALSE)
Error in `[.data.table`(out[["Brier"]][["score"]], , `:=`(IBS, sapply(times,  : 
  attempt access index 3/3 in VECTOR_ELT
Calls: plotBrier ... Score.list -> computePerformance -> [ -> [.data.table
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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/GPTCM.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:42.01, 253.73 + 28.58