* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/JMbayes2.Rcheck’
* using R Under development (unstable) (2025-11-16 r89026)
* 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 ‘JMbayes2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘JMbayes2’ version ‘0.5-7’
* 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 ‘JMbayes2’ can be installed ... [132s/131s] OK
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... [59s/60s] 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 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 examples ... OK
* checking examples with --run-donttest ... [30m/19m] ERROR
Running examples in ‘JMbayes2-Ex.R’ failed
The error most likely occurred in:

> ### Name: jm Methods
> ### Title: Various Methods for Standard Generics
> ### Aliases: methods.jm coef coef.jm fixef fixef.jm ranef ranef.jm terms
> ###   terms.jm model.matrix model.matrix.jm model.frame model.frame.jm
> ###   family family.jm get_links get_links.jm compare_jm
> 
> ### ** Examples
> 
> ## No test: 
> # linear mixed model fits
> fit_lme1 <- lme(log(serBilir) ~ year:sex + age,
+                 random = ~ year | id, data = pbc2)
> 
> fit_lme2 <- lme(prothrombin ~ sex,
+                 random = ~ year | id, data = pbc2)
> 
> # cox model fit
> fit_cox <- coxph(Surv(years, status2) ~ age, data = pbc2.id)
> 
> # joint model fit
> fit_jm <- jm(fit_cox, list(fit_lme1, fit_lme2), time_var = "year",
+     n_chains = 1L, n_iter = 11000L, n_burnin = 1000L)
* 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/JMbayes2.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 24:10.96, 2061.44 + 38.91