* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/flocker.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 ... [22s/27s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/flocker-00install.html' for details.
* checking installed package size ... 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 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 ... [21s/26s] 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 ... [15s/20s] 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 ... [24s/33s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [200s/244s] ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [199s/243s]
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 0.000304 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.04 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: 0.003 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000184 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.84 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: 0.003 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.011 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000176 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.76 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: 0.012 seconds (Warm-up)
Chain 3: 0.01 seconds (Sampling)
Chain 3: 0.022 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000194 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.94 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: 0.003 seconds (Warm-up)
Chain 4: 0.003 seconds (Sampling)
Chain 4: 0.006 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: "/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:
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 ... [14s/19s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR