- 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 the install log 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:
▆
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