• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘familiar/DESCRIPTION’ ... OK
• this is package ‘familiar’ version ‘1.5.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/5s] OK
• 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 ‘familiar’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [3s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/4s] 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 ... [136s/170s] OK
• checking Rd files ... [3s/4s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [3s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [37s/23s] ERROR   Running ‘testthat.R’ [37s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(familiar)   >   > suppressWarnings(   + testthat::test_check("familiar"),   + classes = c("deprecation_warning")   + )   Starting 2 test processes.   Saving _problems/test-sample_weights-4.R   Saving _problems/test-transformation-9.R   [ FAIL 2 | WARN 0 | SKIP 72 | PASS 511 ]      ══ Skipped tests (72) ══════════════════════════════════════════════════════════   • On CRAN (71): 'test-0_plot_calibration.R:3:1', 'test-0_plot_ice_b.R:3:1',     'test-0_plot_ice_a.R:3:1', 'test-0_plot_sample_clustering_a.R:3:1',     'test-0_plot_sample_clustering_b.R:3:1',     'test-0_preprocessing_clustering.R:2:1', 'test-apply.R:2:1',     'test-as_data_object.R:1:1', 'test-batch_normalisation.R:2:1',     'test-collection_labels.R:2:1', 'test-0_vimp_rfsrc_S4.R:8:1',     'test-dynamic_model_loading.R:1:1', 'test-experiment_data.R:2:1',     'test-experimental_design.R:1:1', 'test-export_calibration_info.R:3:1',     'test-export_hyperparameters.R:3:1', 'test-export_ice.R:2:1',     'test-export_risk_stratification_info.R:2:1',     'test-export_prediction_data.R:2:1', 'test-export_sample_clustering.R:2:1',     'test-familiar_data_creation.R:2:1', 'test-function_wrappers.R:1:1',     'test-general_normalisation.R:1:1', 'test-hyperparameter_optimisation.R:2:1',     'test-imputation.R:2:1', 'test-learner_cox_s4.R:6:1',     'test-learner_glm_S4.R:6:1', 'test-learner_glmnet_S4.R:10:1',     'test-learner_mboost_lm_S4.R:5:1', 'test-learner_mboost_tree_S4.R:5:1',     'test-learner_naive_bayes_S4.R:6:1', 'test-learner_ranger_s4.R:7:1',     'test-learner_rfsrc_s4.R:7:1', 'test-learner_survival_regression_S4.R:7:1',     'test-learner_knn_S4.R:6:1', 'test-learner_svm_S4.R:11:1',     'test-learner_xgboost_dart_S4.R:7:1', 'test-learner_xgboost_lm_S4.R:7:1',     'test-learner_xgboost_tree_S4.R:7:1', 'test-metric_auc_roc_S4.R:4:1',     'test-metric_brier_S4.R:4:1', 'test-metric_concordance_index_S4.R:4:1',     'test-metric_regression_S4.R:6:1', 'test-naive_model.R:1:1',     'test-metric_confusion_matrix_metrics_S4.R:6:1',     'test-novelty_isolation_forest_S4.R:6:1', 'test-object_conversion.R:2:1',     'test-novelty_none_S4.R:6:1', 'test-parallel_backend.R:1:1',     'test-plot_auc_curves.R:3:1', 'test-plot_confusion_matrix.R:3:1',     'test-plot_feature_similarity.R:3:1', 'test-plot_decision_curve.R:3:1',     'test-plot_kaplan_meier_curve.R:3:1', 'test-plot_model_performance.R:3:1',     'test-plot_model_ranks.R:2:1',     'test-plot_permutation_variable_importance.R:3:1',     'test-plot_univariate_importance.R:3:1', 'test-predict.R:3:1',     'test-process_time.R:1:1', 'test-stratification.R:1:1',     'test-train_familiar.R:1:1', 'test-subsampling_functions.R:2:1',     'test-vimp_concordance_S4.R:5:1', 'test-vimp_corelearn_S4.R:11:1',     'test-vimp_correlation_S4.R:5:1', 'test-vimp_mutual_information_S4.R:7:1',     'test-vimp_ranger_S4.R:7:1', 'test-vimp_regression_S4.R:8:1',     'test-vimp_glmnet_S4.R:10:1', 'test-vimp_table.R:1:1'   • Testing object updates should be done manually. (1):     'test-update_object.R:1:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-sample_weights.R:4:1'): (code run outside of `test_that()`) ────   Error in ``[.data.table`(temp_data, , `:=`("series_id", seq_len(.N)), by = c("sample_id", "batch_id"))`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─familiar:::test_create_good_data(outcome_type = "binomial") at test-sample_weights.R:4:1    2. ├─familiar::as_data_object(...)    3. └─familiar::as_data_object(...)    4. └─familiar (local) .local(data, ...)    5. └─familiar:::.finish_data_preparation(...)    6. ├─...[]    7. └─data.table:::`[.data.table`(...)   ── Error ('test-transformation.R:7:3'): (code run outside of `test_that()`) ────   Error in ``[.data.table`(data, , `:=`("repetition_id", seq_len(.N)), by = c("sample_id", "batch_id", "series_id", outcome_cols))`: attempt access index 9/9 in VECTOR_ELT   Backtrace:       ▆    1. └─familiar:::test_create_synthetic_series_data(...) at test-transformation.R:7:3    2. ├─familiar::as_data_object(...)    3. └─familiar::as_data_object(...)    4. └─familiar (local) .local(data, ...)    5. └─familiar:::.finish_data_preparation(...)    6. ├─...[]    7. └─data.table:::`[.data.table`(...)      [ FAIL 2 | WARN 0 | SKIP 72 | PASS 511 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/16s] OK
• checking PDF version of manual ... [25s/32s] OK
• checking HTML version of manual ... [43s/58s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR