- using R Under development (unstable) (2024-03-20 r86158)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘bayesnec/DESCRIPTION’ ... OK
- this is package ‘bayesnec’ version ‘2.1.1.0’
- 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 ‘bayesnec’ can be installed ... [73s/190s] OK
See the install log for details.
- 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 ... [11s/25s] OK
- checking whether the package can be loaded with stated dependencies ... [10s/25s] OK
- checking whether the package can be unloaded cleanly ... [10s/26s] OK
- checking whether the namespace can be loaded with stated dependencies ... [10s/22s] OK
- checking whether the namespace can be unloaded cleanly ... [11s/23s] OK
- checking loading without being on the library search path ... [16s/41s] 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 ... [63s/159s] 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 ... [18s/68s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking R/sysdata.rda ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [20s/55s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [13s/22s] ERROR
Running ‘testthat.R’ [12s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(bayesnec)
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.21.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').
Attaching package: 'brms'
The following object is masked from 'package:stats':
ar
Loading required package: ggplot2
>
> test_check("bayesnec")
Error in `FUN()`:
! In path: "/data/gannet/ripley/R/packages/tests-devel/bayesnec.Rcheck/tests/testthat/setup.R"
Caused by error:
! Error in x$terms : $ operator is invalid for atomic vectors
Backtrace:
▆
1. ├─testthat::test_check("bayesnec")
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]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ ├─base::suppressWarnings(...) at tests/testthat/setup.R:25:1
15. │ │ └─base::withCallingHandlers(...)
16. │ ├─base::suppressMessages(pull_out(manec_example, model = "nec4param"))
17. │ │ └─base::withCallingHandlers(...)
18. │ └─bayesnec::pull_out(manec_example, model = "nec4param")
19. │ ├─base::suppressWarnings(...)
20. │ │ └─base::withCallingHandlers(...)
21. │ ├─base::suppressMessages(...)
22. │ │ └─base::withCallingHandlers(...)
23. │ └─bayesnec::expand_nec(...)
24. │ └─bayesnec:::add_criteria(object, loo_controls$fitting, ...)
25. │ ├─base::do.call(add_criterion, loo_args)
26. │ ├─brms (local) `<fn>`(x = `<brmsfit>`, criterion = `<chr>`, model_name = "nec4param")
27. │ └─brms:::add_criterion.brmsfit(...)
28. │ └─brms::do_call(fun, args)
29. │ └─brms:::eval2(call, envir = args, enclos = envir)
30. │ └─base::eval(expr, envir, ...)
31. │ └─base::eval(expr, envir, ...)
32. │ ├─loo::loo(.x1, model_names = .x2)
33. │ └─brms:::loo.brmsfit(.x1, model_names = .x2)
34. │ └─brms::do_call(compute_loolist, args)
35. │ └─brms:::eval2(call, envir = args, enclos = envir)
36. │ └─base::eval(expr, envir, ...)
37. │ └─base::eval(expr, envir, ...)
38. │ └─brms (local) .fun(...)
39. │ └─brms::do_call(compute_loo, args)
40. │ └─brms:::eval2(call, envir = args, enclos = envir)
41. │ └─base::eval(expr, envir, ...)
42. │ └─base::eval(expr, envir, ...)
43. │ └─brms (local) .fun(...)
44. │ └─brms::do_call(paste0(".", criterion), args)
45. │ └─brms:::eval2(call, envir = args, enclos = envir)
46. │ └─base::eval(expr, envir, ...)
47. │ └─base::eval(expr, envir, ...)
48. │ └─brms:::.loo(...)
49. │ └─brms:::prepare_loo_args(...)
50. │ └─brms::do_call(log_lik, ll_args)
51. │ └─brms:::eval2(call, envir = args, enclos = envir)
52. │ └─base::eval(expr, envir, ...)
53. │ └─base::eval(expr, envir, ...)
54. │ ├─rstantools (local) .fun(...)
55. │ └─brms:::log_lik.brmsfit(...)
56. │ ├─rstantools::log_lik(prep, combine = combine, cores = cores)
57. │ └─brms:::log_lik.brmsprep(prep, combine = combine, cores = cores)
58. │ └─brms::get_dpar(object, dpar = dp)
59. │ ├─brms:::predictor(x, i = i, fprep = prep)
60. │ └─brms:::predictor.bprepnl(x, i = i, fprep = prep)
61. │ └─brms:::stop2(eta)
62. │ └─base::stop(..., call. = FALSE)
63. └─base::.handleSimpleError(...)
64. └─testthat (local) h(simpleError(msg, call))
65. └─rlang::abort(...)
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [31s/93s] OK
- checking PDF version of manual ... [11s/32s] 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