* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/E2E.Rcheck’ * using R Under development (unstable) (2025-12-02 r89085) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘E2E/DESCRIPTION’ ... OK * this is package ‘E2E’ version ‘0.1.1’ * 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 ‘E2E’ can be installed ... [20s/20s] 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 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 ... [31s/31s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... [36s/36s] ERROR Running examples in ‘E2E-Ex.R’ failed The error most likely occurred in: > ### Name: imbalance_dia > ### Title: Train an EasyEnsemble Model for Imbalanced Classification > ### Aliases: imbalance_dia > > ### ** Examples > > ## No test: > # 1. Initialize the modeling system > initialize_modeling_system_dia() Diagnostic modeling system already initialized > > # 2. Create an imbalanced toy dataset > set.seed(42) > n_obs <- 100 > n_minority <- 10 > data_imbalanced_toy <- data.frame( + ID = paste0("Sample", 1:n_obs), + Status = c(rep(1, n_minority), rep(0, n_obs - n_minority)), + Feat1 = rnorm(n_obs), + Feat2 = runif(n_obs) + ) > > # 3. Run the EasyEnsemble algorithm > # n_estimators is reduced for a quick example > easyensemble_results <- imbalance_dia( + data = data_imbalanced_toy, + base_model_name = "xb", + n_estimators = 3, + threshold_choices = "f1" + ) Running Imbalance model: EasyEnsemble_dia (base: xb) Loading required package: ggplot2 Loading required package: lattice Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold1: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold2: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold3: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold4: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold5: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, : There were missing values in resampled performance measures. Something is wrong; all the ROC metric values are missing: ROC Sens Spec Min. : NA Min. : NA Min. : NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA Median : NA Median : NA Median : NA Mean :NaN Mean :NaN Mean :NaN 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA Max. : NA Max. : NA Max. : NA NA's :1 NA's :1 NA's :1 Warning in value[[3L]](cond) : Training base model xb for subset 1 failed: Stopping Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold1: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold2: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold3: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold4: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold5: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, : There were missing values in resampled performance measures. Something is wrong; all the ROC metric values are missing: ROC Sens Spec Min. : NA Min. : NA Min. : NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA Median : NA Median : NA Median : NA Mean :NaN Mean :NaN Mean :NaN 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA Max. : NA Max. : NA Max. : NA NA's :1 NA's :1 NA's :1 Warning in value[[3L]](cond) : Training base model xb for subset 2 failed: Stopping Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold1: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold2: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold3: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold4: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in check.custom.obj(params, objective) : Argument 'objective' is only for custom objectives. For built-in objectives, pass the objective under 'params'. This warning will become an error in a future version. Warning: model fit failed for Fold5: nrounds=100, max_depth=3, eta=0.3, gamma=0, colsample_bytree=1, min_child_weight=1, subsample=1 Error in modelFit$xNames <- colnames(x) : ALTLIST classes must provide a Set_elt method [class: XGBAltrepPointerClass, pkg: xgboost] Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo, : There were missing values in resampled performance measures. Something is wrong; all the ROC metric values are missing: ROC Sens Spec Min. : NA Min. : NA Min. : NA 1st Qu.: NA 1st Qu.: NA 1st Qu.: NA Median : NA Median : NA Median : NA Mean :NaN Mean :NaN Mean :NaN 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.: NA Max. : NA Max. : NA Max. : NA NA's :1 NA's :1 NA's :1 Warning in value[[3L]](cond) : Training base model xb for subset 3 failed: Stopping Error in imbalance_dia(data = data_imbalanced_toy, base_model_name = "xb", : No base models were successfully trained. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [85s/108s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘advanced-features.Rmd’ using rmarkdown Quitting from advanced-features.Rmd:102-113 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `bagging_dia()`: ! No base models were successfully trained or made valid predictions. Cannot perform bagging. --- Backtrace: ▆ 1. └─E2E::bagging_dia(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'advanced-features.Rmd' failed with diagnostics: No base models were successfully trained or made valid predictions. Cannot perform bagging. --- failed re-building ‘advanced-features.Rmd’ --- re-building ‘diagnostic-workflow.Rmd’ using rmarkdown Quitting from diagnostic-workflow.Rmd:80-85 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `bagging_dia()`: ! No base models were successfully trained or made valid predictions. Cannot perform bagging. --- Backtrace: ▆ 1. └─E2E::bagging_dia(train_dia, base_model_name = "xb", n_estimators = 5) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'diagnostic-workflow.Rmd' failed with diagnostics: No base models were successfully trained or made valid predictions. Cannot perform bagging. --- failed re-building ‘diagnostic-workflow.Rmd’ --- re-building ‘getting-started.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘getting-started.Rmd’ --- re-building ‘integrated-pipeline.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘integrated-pipeline.Rmd’ --- re-building ‘parameter-reference.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘parameter-reference.Rmd’ --- re-building ‘prognostic-workflow.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘prognostic-workflow.Rmd’ SUMMARY: processing the following files failed: ‘advanced-features.Rmd’ ‘diagnostic-workflow.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/E2E.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 5:17.86, 263.53 + 30.79