* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/EcoEnsemble.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 ‘EcoEnsemble/DESCRIPTION’ ... OK
* this is package ‘EcoEnsemble’ version ‘1.1.2’
* 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 ‘EcoEnsemble’ can be installed ... [50m/14m] 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 ... [9s/16s] 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 ... [8s/10s] OK
* checking loading without being on the library search path ... [12s/21s] OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [42s/80s] 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* 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 ... [8s/15s] OK
* checking examples with --run-donttest ... [30m/32m] ERROR
Running examples in ‘EcoEnsemble-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_mcmc_ensemble_model
> ### Title: Return the compiled ensemble model Stan object.
> ### Aliases: get_mcmc_ensemble_model
> 
> ### ** Examples
> 
> priors <- EnsemblePrior(4)
> mod <- get_mcmc_ensemble_model(priors)
> 
> ensemble_data <- EnsembleData(observations = list(SSB_obs, Sigma_obs),
+                              simulators = list(list(SSB_ewe, Sigma_ewe, "EwE"),
+                                            list(SSB_fs,  Sigma_fs, "FishSUMS"),
+                                            list(SSB_lm,  Sigma_lm, "LeMans"),
+                                            list(SSB_miz, Sigma_miz, "mizer")),
+                               priors = priors)
> ## No test: 
> out <- rstan::sampling(mod, ensemble_data@stan_input, chains = 1)

SAMPLING FOR MODEL 'ensemble_model_hierarchical' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.081728 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 817.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [36s/37s]
 [36s/38s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [90s/93s] 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, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/EcoEnsemble.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 55:14.19, 4919.17 + 226.08