* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/flocker.Rcheck’ * using R Under development (unstable) (2025-02-26 r87830) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘flocker/DESCRIPTION’ ... OK * this is package ‘flocker’ version ‘1.0-0’ * 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 ‘flocker’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/flocker-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [12s/17s] OK * checking Rd files ... [0s/1s] 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 ... [10s/11s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [15s/18s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed log_lik_flocker 6.622 0.266 8.582 flocker_standata 4.353 0.301 5.263 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [157s/195s] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [156s/194s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(flocker) > > test_check("flocker") Formatting data for a single-season occupancy model. For details, see make_flocker_data_static. All warnings and error messages should be interpreted in the context of make_flocker_data_static Compiling Stan program... Start sampling SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000255 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.55 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 8 [ 12%] (Warmup) Chain 1: Iteration: 2 / 8 [ 25%] (Warmup) Chain 1: Iteration: 3 / 8 [ 37%] (Warmup) Chain 1: Iteration: 4 / 8 [ 50%] (Warmup) Chain 1: Iteration: 5 / 8 [ 62%] (Sampling) Chain 1: Iteration: 6 / 8 [ 75%] (Sampling) Chain 1: Iteration: 7 / 8 [ 87%] (Sampling) Chain 1: Iteration: 8 / 8 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.002 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.005 seconds (Total) Chain 1: SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000145 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.45 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 8 [ 12%] (Warmup) Chain 2: Iteration: 2 / 8 [ 25%] (Warmup) Chain 2: Iteration: 3 / 8 [ 37%] (Warmup) Chain 2: Iteration: 4 / 8 [ 50%] (Warmup) Chain 2: Iteration: 5 / 8 [ 62%] (Sampling) Chain 2: Iteration: 6 / 8 [ 75%] (Sampling) Chain 2: Iteration: 7 / 8 [ 87%] (Sampling) Chain 2: Iteration: 8 / 8 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 0.002 seconds (Warm-up) Chain 2: 0.005 seconds (Sampling) Chain 2: 0.007 seconds (Total) Chain 2: SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 0.000159 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.59 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: WARNING: No variance estimation is Chain 3: performed for num_warmup < 20 Chain 3: Chain 3: Iteration: 1 / 8 [ 12%] (Warmup) Chain 3: Iteration: 2 / 8 [ 25%] (Warmup) Chain 3: Iteration: 3 / 8 [ 37%] (Warmup) Chain 3: Iteration: 4 / 8 [ 50%] (Warmup) Chain 3: Iteration: 5 / 8 [ 62%] (Sampling) Chain 3: Iteration: 6 / 8 [ 75%] (Sampling) Chain 3: Iteration: 7 / 8 [ 87%] (Sampling) Chain 3: Iteration: 8 / 8 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 0.008 seconds (Warm-up) Chain 3: 0.007 seconds (Sampling) Chain 3: 0.015 seconds (Total) Chain 3: SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 0.000115 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds. Chain 4: Adjust your expectations accordingly! Chain 4: Chain 4: Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4: Chain 4: Iteration: 1 / 8 [ 12%] (Warmup) Chain 4: Iteration: 2 / 8 [ 25%] (Warmup) Chain 4: Iteration: 3 / 8 [ 37%] (Warmup) Chain 4: Iteration: 4 / 8 [ 50%] (Warmup) Chain 4: Iteration: 5 / 8 [ 62%] (Sampling) Chain 4: Iteration: 6 / 8 [ 75%] (Sampling) Chain 4: Iteration: 7 / 8 [ 87%] (Sampling) Chain 4: Iteration: 8 / 8 [100%] (Sampling) Chain 4: Chain 4: Elapsed Time: 0.002 seconds (Warm-up) Chain 4: 0.002 seconds (Sampling) Chain 4: 0.004 seconds (Total) Chain 4: Formatting data for a single-season multispecies occupancy model with data augmentation for never-observed species. For details, see make_flocker_data_augmented. 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Compiling Stan program... 0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function at c$ (<input>:5378:79) at dIb (<input>:25505:6) Error in `FUN()`: ! In path: "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/flocker.Rcheck/tests/testthat/setup.R" Caused by error in `model_cppcode$errors`: ! $ operator is invalid for atomic vectors Backtrace: ▆ 1. ├─testthat::test_check("flocker") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─testthat:::test_files_setup_state(...) 6. │ └─testthat::source_test_setup(".", env) 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 8. │ └─base::lapply(...) 9. │ └─testthat (local) FUN(X[[i]], ...) 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) 11. │ ├─base::withCallingHandlers(...) 12. │ └─base::eval(exprs, env) 13. │ └─base::eval(exprs, env) 14. │ ├─base::suppressWarnings(...) at tests/testthat/setup.R:6:1 15. │ │ └─base::withCallingHandlers(...) 16. │ └─flocker::flock(...) at tests/testthat/setup.R:31:3 17. │ └─flocker:::flock_(...) 18. │ └─flocker:::flocker_fit_code_util(...) 19. │ └─brms::brm(...) 20. │ └─brms::do_call(compile_model, compile_args) 21. │ └─brms:::eval2(call, envir = args, enclos = envir) 22. │ └─base::eval(expr, envir, ...) 23. │ └─base::eval(expr, envir, ...) 24. │ └─brms (local) .fun(...) 25. │ └─brms (local) .compile_model(model, ...) 26. │ ├─brms:::eval_silent(...) 27. │ │ └─base::eval(expr, envir) 28. │ │ └─base::eval(expr, envir) 29. │ └─brms::do_call(rstan::stan_model, args) 30. │ └─brms:::eval2(call, envir = args, enclos = envir) 31. │ └─base::eval(expr, envir, ...) 32. │ └─base::eval(expr, envir, ...) 33. │ └─rstan (local) .fun(model_code = .x1) 34. │ └─rstan::stanc(...) 35. └─base::.handleSimpleError(...) 36. └─testthat (local) h(simpleError(msg, call)) 37. └─rlang::abort(...) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [9s/12s] OK * checking PDF version of manual ... [5s/6s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR