Last updated on 2025-02-22 04:51:12 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0-0 | 13.35 | 241.39 | 254.74 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0-0 | 9.39 | 844.85 | 854.24 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0-0 | 353.31 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0-0 | 1954.95 | OK | |||
| r-devel-macos-arm64 | 1.0-0 | 404.00 | OK | |||
| r-devel-macos-x86_64 | 1.0-0 | 1424.00 | OK | |||
| r-devel-windows-x86_64 | 1.0-0 | 13.00 | 882.00 | 895.00 | OK | |
| r-patched-linux-x86_64 | 1.0-0 | 11.97 | 1113.79 | 1125.76 | OK | |
| r-release-linux-x86_64 | 1.0-0 | 12.64 | 1174.62 | 1187.26 | OK | |
| r-release-macos-arm64 | 1.0-0 | 376.00 | OK | |||
| r-release-macos-x86_64 | 1.0-0 | 1064.00 | OK | |||
| r-release-windows-x86_64 | 1.0-0 | 14.00 | 902.00 | 916.00 | OK | |
| r-oldrel-macos-arm64 | 1.0-0 | 341.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0-0 | 646.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0-0 | 19.00 | 1191.00 | 1210.00 | OK |
Version: 1.0-0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [158s/192s]
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 0.000233 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.33 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 0.000115 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.15 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 0.000119 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.19 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: 0.006 seconds (Sampling)
Chain 3: 0.014 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
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0-0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [196s/247s]
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 0.000383 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.83 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: 0.008 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.022 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000255 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.55 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: 0.02 seconds (Warm-up)
Chain 2: 0.024 seconds (Sampling)
Chain 2: 0.044 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000227 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 2.27 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: 0.028 seconds (Warm-up)
Chain 3: 0.023 seconds (Sampling)
Chain 3: 0.051 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000255 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 2.55 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: 0.012 seconds (Warm-up)
Chain 4: 0.008 seconds (Sampling)
Chain 4: 0.02 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
Error in `FUN()`:
! In path: "/data/gannet/ripley/R/packages/tests-clang/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
Flavor: r-devel-linux-x86_64-fedora-clang