* using log directory ‘/srv/hornik/tmp/CRAN/bayesdfa.Rcheck’ * using R Under development (unstable) (2024-02-25 r85988) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘bayesdfa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bayesdfa’ version ‘1.3.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] Note_to_CRAN_maintainers Maintainer: ‘Eric J. Ward ’ * 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 ‘bayesdfa’ can be installed ... [312s/310s] OK * used C++ compiler: ‘Debian clang version 17.0.6 (5)’ * checking C++ specification ... OK Not all R platforms support C++17 * checking package directory ... OK * checking for future file timestamps ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s/2s] OK * checking whether the package can be loaded with stated dependencies ... [3s/2s] OK * checking whether the package can be unloaded cleanly ... [3s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/2s] OK * checking whether the namespace can be unloaded cleanly ... [3s/2s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking use of S3 registration ... 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 ... [15s/13s] OK * checking Rd files ... [0s/0s] 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 pragmas in C/C++ headers and code ... 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/8s] ERROR Running examples in ‘bayesdfa-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: find_regimes > ### Title: Fit multiple models with differing numbers of regimes to trend > ### data > ### Aliases: find_regimes > > ### ** Examples > > data(Nile) > find_regimes(log(Nile), iter = 50, chains = 1, max_regimes = 2) SAMPLING FOR MODEL 'regime_1' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 1.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: There aren't enough warmup iterations to fit the Chain 1: three stages of adaptation as currently configured. Chain 1: Reducing each adaptation stage to 15%/75%/10% of Chain 1: the given number of warmup iterations: Chain 1: init_buffer = 3 Chain 1: adapt_window = 20 Chain 1: term_buffer = 2 Chain 1: Chain 1: Iteration: 1 / 50 [ 2%] (Warmup) Chain 1: Iteration: 5 / 50 [ 10%] (Warmup) Chain 1: Iteration: 10 / 50 [ 20%] (Warmup) Chain 1: Iteration: 15 / 50 [ 30%] (Warmup) Chain 1: Iteration: 20 / 50 [ 40%] (Warmup) Chain 1: Iteration: 25 / 50 [ 50%] (Warmup) Chain 1: Iteration: 26 / 50 [ 52%] (Sampling) Chain 1: Iteration: 30 / 50 [ 60%] (Sampling) Chain 1: Iteration: 35 / 50 [ 70%] (Sampling) Chain 1: Iteration: 40 / 50 [ 80%] (Sampling) Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) Chain 1: Iteration: 50 / 50 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0 seconds (Warm-up) Chain 1: 0 seconds (Sampling) Chain 1: 0 seconds (Total) Chain 1: Warning: The largest R-hat is 1.07, indicating chains have not mixed. Running the chains for more iterations may help. See https://mc-stan.org/misc/warnings.html#r-hat Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. Running the chains for more iterations may help. See https://mc-stan.org/misc/warnings.html#bulk-ess Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. Running the chains for more iterations may help. See https://mc-stan.org/misc/warnings.html#tail-ess Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details. Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details. Error in loo::pareto_k_table(looic)["(0.7, 1]", "Count"] : subscript out of bounds Calls: find_regimes Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [5s/5s] OK Running ‘testthat.R’ [4s/4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [67s/67s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR