* using log directory ‘/Users/ripley/R/packages/tests-devel/CimpleG.Rcheck’
* using R Under development (unstable) (2025-12-03 r89090)
* using platform: aarch64-apple-darwin25.1.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘CimpleG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CimpleG’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘EpiDISH’
* 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 ‘CimpleG’ can be installed ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’ [64s/33s]
 [64s/34s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CimpleG)
  ---------------------
  CimpleG version 1.0.0
  ---------------------
  > 
  > test_check("CimpleG")
  Starting 2 test processes.
  > test-CimpleG.R: Warning: stack imbalance in '::', 115 then 117
  > test-CimpleG.R: Warning: stack imbalance in '<-', 113 then 115
  > test-CimpleG.R: Setting options('download.file.method.GEOquery'='auto')
  > test-CimpleG.R: Setting options('GEOquery.inmemory.gpl'=FALSE)
  > test-CimpleG.R: Warning: stack imbalance in '{', 109 then 111
  Saving _problems/test3-CimpleG-xgboost-13.R
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test1-CimpleG-decisiontree.R:3:3', 'test1-CimpleG-nnet.R:3:3',
    'test1-CimpleG-rf.R:3:3'
  • parallel not working properly locally (1): 'test8-CimpleG-parallel.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test3-CimpleG-xgboost.R:5:3'): signatures are generated w/ xgboost ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::map(.x = target_columns, .f = work_helper)`: i In index: 1.
  Caused by error in `x$callbacks <- purrr::map(x$callbacks, function(x) as.function(c(formals(x),
    body(x)), env = rlang::base_env()))`:
  ! ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost]
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test3-CimpleG-xgboost.R:5:3
    2. │ └─base::withCallingHandlers(...)
    3. ├─base::suppressMessages(...)
    4. │ └─base::withCallingHandlers(...)
    5. ├─CimpleG::CimpleG(...)
    6. ├─CimpleG:::CimpleG.matrix(...)
    7. │ └─CimpleG:::CimpleG_main(...)
    8. │   ├─purrr::map(.x = target_columns, .f = work_helper) %>% ...
    9. │   └─purrr::map(.x = target_columns, .f = work_helper)
   10. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
   11. │       ├─purrr:::with_indexed_errors(...)
   12. │       │ └─base::withCallingHandlers(...)
   13. │       ├─purrr:::call_with_cleanup(...)
   14. │       └─CimpleG (local) .f(.x[[i]], ...)
   15. │         └─CimpleG:::train_general_model(...)
   16. │           └─cimpleg_final_model %>% butcher::axe_call() %>% butcher::axe_env()
   17. ├─butcher::axe_env(.)
   18. ├─workflows:::axe_env.workflow(.)
   19. │ ├─butcher::axe_env(fit, verbose = verbose, ...)
   20. │ └─butcher:::axe_env.model_fit(fit, verbose = verbose, ...)
   21. │   ├─butcher::axe_env(x$fit, verbose = verbose, ...)
   22. │   └─butcher:::axe_env.xgb.Booster(x$fit, verbose = verbose, ...)
   23. └─base::.handleSimpleError(...)
   24.   └─purrr (local) h(simpleError(msg, call))
   25.     └─cli::cli_abort(...)
   26.       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 62 ]
  Error:
  ! Test failures.
  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 ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/ripley/R/packages/tests-devel/CimpleG.Rcheck/00check.log’
for details.

       89.06 real        97.93 user        12.09 sys