* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/rbmi.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 ‘rbmi/DESCRIPTION’ ... OK
* this is package ‘rbmi’ version ‘1.4.0’
* 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 ‘rbmi’ can be installed ... [17s/21s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/rbmi-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 whether startup messages can be suppressed ... 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 ... [23s/28s] 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [182s/331s] ERROR
  Running ‘testthat.R’ [181s/330s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rbmi)
  > 
  > test_check("rbmi")
  0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function
      at c$ (<input>:5378:79)
      at dIb (<input>:25505:6)
  
  mmrm() registered as emmeans extension
  0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function
      at c$ (<input>:5378:79)
      at dIb (<input>:25505:6)
  
  0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function
      at c$ (<input>:5378:79)
      at dIb (<input>:25505:6)
  
  0,248,Js_of_ocaml__Js.Error,18,TypeError: not a function
      at c$ (<input>:5378:79)
      at dIb (<input>:25505:6)
  
  [ FAIL 4 | WARN 0 | SKIP 15 | PASS 1261 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-mmrm.R:337:5'
  • is_full_test() is not TRUE (14): 'test-draws.R:115:5',
    'test-fullusage.R:43:5', 'test-fullusage.R:117:5', 'test-fullusage.R:209:5',
    'test-fullusage.R:300:5', 'test-fullusage.R:431:5', 'test-fullusage.R:520:5',
    'test-fullusage.R:675:5', 'test-mcmc.R:327:5', 'test-mcmc.R:504:5',
    'test-mcmc.R:635:5', 'test-parallel.R:8:5', 'test-reproducibility.R:9:5',
    'test-reproducibility.R:135:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-draws.R:144:9'): bayes ─────────────────────────────────────────
  Error in `model_cppcode$errors`: $ operator is invalid for atomic vectors
  Backtrace:
      â–†
   1. ├─base::suppressWarnings(...) at test-draws.R:143:5
   2. │ └─base::withCallingHandlers(...)
   3. ├─rbmi::draws(d$dat, d$dat_ice, d$vars, meth, quiet = TRUE) at test-draws.R:144:9
   4. └─rbmi:::draws.bayes(d$dat, d$dat_ice, d$vars, meth, quiet = TRUE)
   5.   └─rbmi:::fit_mcmc(...)
   6.     └─rbmi:::get_stan_model()
   7.       └─rstan::stan_model(file = model_file, auto_write = TRUE, model_name = "rbmi_mmrm")
   8.         └─rstan::stanc(...)
  ── Error ('test-mcmc.R:108:13'): Verbose suppression works ─────────────────────
  Error in `model_cppcode$errors`: $ operator is invalid for atomic vectors
  Backtrace:
       â–†
    1. ├─base::suppressWarnings(...) at test-mcmc.R:106:5
    2. │ └─base::withCallingHandlers(...)
    3. ├─utils::capture.output(...) at test-mcmc.R:107:9
    4. │ └─base::withVisible(...elt(i))
    5. ├─rbmi::draws(...) at test-mcmc.R:108:13
    6. └─rbmi:::draws.bayes(...)
    7.   └─rbmi:::fit_mcmc(...)
    8.     └─rbmi:::get_stan_model()
    9.       └─rstan::stan_model(file = model_file, auto_write = TRUE, model_name = "rbmi_mmrm")
   10.         └─rstan::stanc(...)
  ── Error ('test-print.R:102:9'): print - bayesian ──────────────────────────────
  Error in `model_cppcode$errors`: $ operator is invalid for atomic vectors
  Backtrace:
      â–†
   1. ├─base::suppressWarnings(...) at test-print.R:101:5
   2. │ └─base::withCallingHandlers(...)
   3. ├─rbmi::draws(...) at test-print.R:102:9
   4. └─rbmi:::draws.bayes(...)
   5.   └─rbmi:::fit_mcmc(...)
   6.     └─rbmi:::get_stan_model()
   7.       └─rstan::stan_model(file = model_file, auto_write = TRUE, model_name = "rbmi_mmrm")
   8.         └─rstan::stanc(...)
  ── Error ('test-reproducibility.R:123:9'): bayes - set.seed produces identical results ──
  Error in `model_cppcode$errors`: $ operator is invalid for atomic vectors
  Backtrace:
      â–†
   1. ├─base::suppressWarnings(...) at test-reproducibility.R:122:5
   2. │ └─base::withCallingHandlers(...)
   3. ├─rbmi::draws(dat, dat_ice, vars, meth, quiet = TRUE) at test-reproducibility.R:123:9
   4. └─rbmi:::draws.bayes(dat, dat_ice, vars, meth, quiet = TRUE)
   5.   └─rbmi:::fit_mcmc(...)
   6.     └─rbmi:::get_stan_model()
   7.       └─rstan::stan_model(file = model_file, auto_write = TRUE, model_name = "rbmi_mmrm")
   8.         └─rstan::stanc(...)
  
  [ FAIL 4 | WARN 0 | SKIP 15 | PASS 1261 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [18s/23s] OK
* checking HTML version of manual ... [9s/22s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR