- using R Under development (unstable) (2025-12-06 r89118)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘tidysdm/DESCRIPTION’ ... OK
- this is package ‘tidysdm’ version ‘1.0.3’
- 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 ‘tidysdm’ can be installed ... [48s/50s] 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 ... [10s/10s] 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 ... [10s/10s] OK
- checking whether startup messages can be suppressed ... [10s/10s] 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 ... [51s/53s] 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 ... INFO
Error loading dataset 'lacerta_ensemble':
Error in xgb.get.handle(model) :
'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
- 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 ... [59s/60s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [120s/122s] ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [119s/121s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(tidysdm)
Loading required package: tidymodels
── Attaching packages ────────────────────────────────────── tidymodels 1.4.1 ──
✔ broom 1.0.11 ✔ recipes 1.3.1
✔ dials 1.4.2 ✔ rsample 1.3.1
✔ dplyr 1.1.4 ✔ tailor 0.1.0
✔ ggplot2 4.0.1 ✔ tidyr 1.3.1
✔ infer 1.0.9 ✔ tune 2.0.1
✔ modeldata 1.5.1 ✔ workflows 1.3.0
✔ parsnip 1.4.0 ✔ workflowsets 1.1.1
✔ purrr 1.2.0 ✔ yardstick 1.3.2
── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
✖ purrr::discard() masks scales::discard()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
✖ recipes::step() masks stats::step()
Loading required package: spatialsample
>
> test_check("tidysdm")
Attaching package: 'plotrix'
The following object is masked from 'package:scales':
rescale
i Creating pre-processing data to finalize 1 unknown parameter: "mtry"
Saving _problems/test_explain_tidysdm-121.R
Saving _problems/test_overlap_niche-14.R
Saving _problems/test_predict_raster-8.R
i Creating pre-processing data to finalize 1 unknown parameter: "mtry"
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 314 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test_filter_collinear.R:2:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_explain_tidysdm.R:121:3'): explain_tidysdm works with response provided directly ──
Error in `xgb.get.handle(model)`: 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Backtrace:
▆
1. ├─testthat::expect_true(all.equal(test_explainer, test_explainer_y)) at test_explain_tidysdm.R:121:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::all.equal(test_explainer, test_explainer_y)
5. └─base::all.equal.default(test_explainer, test_explainer_y)
6. └─base::all.equal.list(target, current, ...)
7. ├─base::all.equal(...)
8. └─base::all.equal.default(...)
9. └─base::all.equal.list(target, current, ...)
10. ├─base::all.equal(...)
11. └─base::all.equal.list(...)
12. ├─base::all.equal(...)
13. └─base::all.equal.default(...)
14. └─base::all.equal.list(target, current, ...)
15. ├─base::all.equal(...)
16. └─base::all.equal.default(...)
17. └─base::all.equal.list(target, current, ...)
18. ├─base::all.equal(...)
19. └─base::all.equal.default(...)
20. └─base::all.equal.list(target, current, ...)
21. ├─base::all.equal(...)
22. └─base::all.equal.default(...)
23. └─base::all.equal.list(target, current, ...)
24. └─base::attr.all.equal(target, current, ...)
25. ├─base::length(target)
26. └─xgboost:::length.xgb.Booster(target)
27. └─xgboost::xgb.get.num.boosted.rounds(x)
28. └─xgboost:::xgb.get.handle(model)
── Error ('test_overlap_niche.R:14:3'): niche_overlap quantifies difference between rasters ──
Error in `xgb.get.handle(object)`: 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Backtrace:
▆
1. ├─tidysdm::predict_raster(lacerta_ensemble, climate_present) at test_overlap_niche.R:14:3
2. ├─tidysdm:::predict_raster.default(lacerta_ensemble, climate_present)
3. │ ├─stats::predict(object, rast_sub_values, ...)
4. │ └─tidysdm:::predict.simple_ensemble(object, rast_sub_values, ...)
5. │ └─base::lapply(...)
6. │ ├─stats (local) FUN(X[[i]], ...)
7. │ └─workflows:::predict.workflow(X[[i]], ...)
8. │ ├─stats::predict(fit, new_data, type = type, opts = opts, ...)
9. │ └─parsnip::predict.model_fit(...)
10. │ ├─parsnip:::predict_classprob(...)
11. │ └─parsnip::predict_classprob.model_fit(...)
12. │ └─rlang::eval_tidy(pred_call)
13. └─parsnip::xgb_predict(object = object$fit, new_data = new_data)
14. ├─stats::predict(object, new_data, ...)
15. └─xgboost:::predict.xgb.Booster(object, new_data, ...)
16. └─xgboost:::xgb.best_iteration(object)
17. └─xgboost::xgb.attr(bst, "best_iteration")
18. └─xgboost:::xgb.get.handle(object)
── Error ('test_predict_raster.R:8:3'): predict_raster works correctly in chunks ──
Error in `xgb.get.handle(object)`: 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Backtrace:
▆
1. ├─tidysdm::predict_raster(lacerta_ensemble, climate_future) at test_predict_raster.R:8:3
2. ├─tidysdm:::predict_raster.default(lacerta_ensemble, climate_future)
3. │ ├─stats::predict(object, rast_sub_values, ...)
4. │ └─tidysdm:::predict.simple_ensemble(object, rast_sub_values, ...)
5. │ └─base::lapply(...)
6. │ ├─stats (local) FUN(X[[i]], ...)
7. │ └─workflows:::predict.workflow(X[[i]], ...)
8. │ ├─stats::predict(fit, new_data, type = type, opts = opts, ...)
9. │ └─parsnip::predict.model_fit(...)
10. │ ├─parsnip:::predict_classprob(...)
11. │ └─parsnip::predict_classprob.model_fit(...)
12. │ └─rlang::eval_tidy(pred_call)
13. └─parsnip::xgb_predict(object = object$fit, new_data = new_data)
14. ├─stats::predict(object, new_data, ...)
15. └─xgboost:::predict.xgb.Booster(object, new_data, ...)
16. └─xgboost:::xgb.best_iteration(object)
17. └─xgboost::xgb.attr(bst, "best_iteration")
18. └─xgboost:::xgb.get.handle(object)
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 314 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [401s/409s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘a0_tidysdm_overview.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘a0_tidysdm_overview.Rmd’
--- re-building ‘a1_palaeodata_application.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘a1_palaeodata_application.Rmd’
--- re-building ‘a2_tidymodels_additions.Rmd’ using rmarkdown
Quitting from a2_tidymodels_additions.Rmd:65-69 [vip]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgb.get.handle()`:
! 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
---
Backtrace:
▆
1. ├─DALEX::model_parts(explainer = explainer_lacerta_ens)
2. │ ├─ingredients::feature_importance(...)
3. │ └─ingredients:::feature_importance.explainer(...)
4. │ └─ingredients:::feature_importance.default(...)
5. │ └─base::replicate(B, loss_after_permutation())
6. │ └─base::sapply(...)
7. │ └─base::lapply(X = X, FUN = FUN, ...)
8. │ └─ingredients (local) FUN(X[[i]], ...)
9. │ └─ingredients (local) loss_after_permutation()
10. │ ├─DALEX (local) loss_function(observed, predict_function(x, sampled_data))
11. │ │ └─base::tapply(observed, predicted, sum)
12. │ └─tidysdm (local) predict_function(x, sampled_data)
13. │ ├─stats::predict(model, newdata)
14. │ └─tidysdm:::predict.simple_ensemble(model, newdata)
15. │ └─base::lapply(...)
16. │ ├─stats (local) FUN(X[[i]], ...)
17. │ └─workflows:::predict.workflow(X[[i]], ...)
18. │ ├─stats::predict(fit, new_data, type = type, opts = opts, ...)
19. │ └─parsnip::predict.model_fit(...)
20. │ ├─parsnip:::predict_classprob(...)
21. │ └─parsnip::predict_classprob.model_fit(...)
22. │ └─rlang::eval_tidy(pred_call)
23. └─parsnip::xgb_predict(object = object$fit, new_data = new_data)
24. ├─stats::predict(object, new_data, ...)
25. └─xgboost:::predict.xgb.Booster(object, new_data, ...)
26. └─xgboost:::xgb.best_iteration(object)
27. └─xgboost::xgb.attr(bst, "best_iteration")
28. └─xgboost:::xgb.get.handle(object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a2_tidymodels_additions.Rmd' failed with diagnostics:
'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
--- failed re-building ‘a2_tidymodels_additions.Rmd’
--- re-building ‘a3_troubleshooting.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘a3_troubleshooting.Rmd’
SUMMARY: processing the following file failed:
‘a2_tidymodels_additions.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [11s/12s] OK
- checking HTML version of manual ... [11s/11s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 ERRORs