* 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.  All warnings and error messages should be interpreted in the context of make_flocker_data_augmented
  formatting rep indices
  
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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:
       â–†
    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