* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/occumb.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 ‘occumb/DESCRIPTION’ ... OK * this is package ‘occumb’ version ‘1.2.1’ * 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 ‘occumb’ can be installed ... 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 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 ... [13s/14s] 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 R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... [30m/30m] ERROR Running examples in ‘occumb-Ex.R’ failed The error most likely occurred in: > ### Name: eval_util_R > ### Title: Expected utility for regional species diversity assessments. > ### Aliases: eval_util_R > > ### ** Examples > > ## No test: > set.seed(1) > > # Generate a random dataset (20 species * 2 sites * 2 reps) > I <- 20 # Number of species > J <- 2 # Number of sites > K <- 2 # Number of replicates > data <- occumbData( + y = array(sample.int(I * J * K), dim = c(I, J, K))) > > # Fitting a null model > fit <- occumb(data = data) Processing function input....... Done. Compiling model graph Resolving undeclared variables Allocating nodes Graph information: Observed stochastic nodes: 4 Unobserved stochastic nodes: 229 Total graph size: 673 Initializing model Adaptive phase..... Adaptive phase complete Burn-in phase, 10000 iterations x 4 chains Sampling from joint posterior, 10000 iterations x 4 chains Calculating statistics....... Done. > > ## Estimate expected utility > # Arbitrary J, K, and N values > (util1 <- eval_util_R(expand.grid(J = 1:3, K = 1:3, N = c(1E3, 1E4, 1E5)), + fit)) J K N Utility 1 1 1 1e+03 19.80640 2 2 1 1e+03 19.97425 3 3 1 1e+03 19.99291 4 1 2 1e+03 19.88613 5 2 2 1e+03 19.97950 6 3 2 1e+03 19.99450 7 1 3 1e+03 19.88699 8 2 3 1e+03 19.98400 9 3 3 1e+03 19.99450 10 1 1 1e+04 19.84006 11 2 1 1e+04 19.97569 12 3 1 1e+04 19.99100 13 1 2 1e+04 19.89600 14 2 2 1e+04 19.97875 15 3 2 1e+04 19.99200 16 1 3 1e+04 19.89425 17 2 3 1e+04 19.98425 18 3 3 1e+04 19.99150 19 1 1 1e+05 19.84624 20 2 1 1e+05 19.97525 21 3 1 1e+05 19.99075 22 1 2 1e+05 19.88575 23 2 2 1e+05 19.97850 24 3 2 1e+05 19.99250 25 1 3 1e+05 19.88675 26 2 3 1e+05 19.97975 27 3 3 1e+05 19.99325 > > # J, K, and N values under specified budget and cost > (util2 <- eval_util_R(list_cond_R(budget = 50000, + lambda1 = 0.01, + lambda2 = 5000, + lambda3 = 5000), + fit)) budget lambda1 lambda2 lambda3 J K N Utility 1 50000 0.01 5000 5000 1 1 4000000.00 19.83575 2 50000 0.01 5000 5000 2 1 1500000.00 19.97650 3 50000 0.01 5000 5000 3 1 666666.67 19.99425 4 50000 0.01 5000 5000 4 1 250000.00 19.99675 5 50000 0.01 5000 5000 1 2 1750000.00 19.89075 6 50000 0.01 5000 5000 2 2 500000.00 19.98075 7 50000 0.01 5000 5000 3 2 83333.33 19.99250 8 50000 0.01 5000 5000 1 3 1000000.00 19.89250 9 50000 0.01 5000 5000 2 3 166666.67 19.98100 10 50000 0.01 5000 5000 1 4 625000.00 19.89600 11 50000 0.01 5000 5000 1 5 400000.00 19.88925 12 50000 0.01 5000 5000 1 6 250000.00 19.90025 13 50000 0.01 5000 5000 1 7 142857.14 19.89300 14 50000 0.01 5000 5000 1 8 62500.00 19.88900 > > # K values restricted > (util3 <- eval_util_R(list_cond_R(budget = 50000, + lambda1 = 0.01, + lambda2 = 5000, + lambda3 = 5000, + K = 1:5), + fit)) budget lambda1 lambda2 lambda3 J K N Utility 1 50000 0.01 5000 5000 1 1 4000000.00 19.85850 2 50000 0.01 5000 5000 2 1 1500000.00 19.97550 3 50000 0.01 5000 5000 3 1 666666.67 19.99100 4 50000 0.01 5000 5000 4 1 250000.00 19.99500 5 50000 0.01 5000 5000 1 2 1750000.00 19.90200 6 50000 0.01 5000 5000 2 2 500000.00 19.97850 7 50000 0.01 5000 5000 3 2 83333.33 19.99400 8 50000 0.01 5000 5000 1 3 1000000.00 19.88375 9 50000 0.01 5000 5000 2 3 166666.67 19.98100 10 50000 0.01 5000 5000 1 4 625000.00 19.89225 11 50000 0.01 5000 5000 1 5 400000.00 19.89425 > > # J and K values restricted > (util4 <- eval_util_R(list_cond_R(budget = 50000, + lambda1 = 0.01, + lambda2 = 5000, + lambda3 = 5000, + J = 1:3, K = 1:5), + fit)) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ [146s/149s] [147s/150s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [19s/21s] 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/occumb.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 34:25.29, 2004.27 + 27.75