* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/familiar.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘familiar/DESCRIPTION’ ... OK
* this is package ‘familiar’ version ‘1.4.6’
* 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 ‘familiar’ can be installed ... [121s/157s] 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 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 ... [209s/267s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [144s/84s]
 [144s/85s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familiar)
  > 
  > test_check("familiar")
  Starting 2 test processes
  [ FAIL 8 | WARN 0 | SKIP 65 | PASS 3551 ]
  
  ══ Skipped tests (65) ══════════════════════════════════════════════════════════
  • On CRAN (64): 'test-0_plot_calibration.R:2:1', 'test-0_plot_ice_b.R:2:1',
    'test-0_plot_ice_a.R:2:1', 'test-0_plot_sample_clustering_a.R:2:1',
    'test-0_plot_sample_clustering_b.R:2:1',
    '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-0_vimp_rfsrc_S4.R:5:1', 'test-dynamic_model_loading.R:1:1',
    'test-experiment_data.R:2:1', 'test-experimental_design.R:1:1',
    'test-export_calibration_info.R:2:1', 'test-export_hyperparameters.R:2:1',
    'test-export_ice.R:2:1', 'test-export_prediction_data.R:2:1',
    'test-export_risk_stratification_info.R:2:1',
    'test-export_sample_clustering.R:2:1', 'test-familiar_data_creation.R:2:1',
    'test-function_wrappers.R:1:1', 'test-hyperparameter_optimisation.R:2:1',
    'test-imputation.R:2:1', 'test-learner_cox_s4.R:5:1',
    'test-learner_glm_S4.R:5:1', 'test-learner_glmnet_S4.R:7:1',
    'test-learner_knn_S4.R:5:1', 'test-learner_mboost_lm_S4.R:5:1',
    'test-learner_mboost_tree_S4.R:5:1', 'test-learner_naive_bayes_S4.R:5:1',
    'test-learner_ranger_s4.R:5:1', 'test-learner_rfsrc_s4.R:5:1',
    'test-learner_survival_regression_S4.R:5:1', 'test-learner_svm_S4.R:7:1',
    'test-learner_xgboost_dart_S4.R:5:1', 'test-learner_xgboost_lm_S4.R:5:1',
    'test-learner_xgboost_tree_S4.R:5:1',
    'test-metric_confusion_matrix_metrics_S4.R:80:1',
    'test-metric_regression_S4.R:55:1', 'test-naive_model.R:1:1',
    'test-novelty_isolation_forest_S4.R:5:1', 'test-novelty_none_S4.R:5:1',
    'test-object_conversion.R:2:1', 'test-parallel_backend.R:1:1',
    'test-plot_auc_curves.R:2:1', 'test-plot_confusion_matrix.R:2:1',
    'test-plot_decision_curve.R:2:1', 'test-plot_feature_similarity.R:2:1',
    'test-plot_kaplan_meier_curve.R:2:1', 'test-plot_model_performance.R:2:1',
    'test-plot_model_ranks.R:2:1',
    'test-plot_permutation_variable_importance.R:2:1',
    'test-plot_univariate_importance.R:2:1', 'test-predict.R:2:1',
    'test-process_time.R:1:1', 'test-subsampling_functions.R:2:1',
    'test-train_familiar.R:1:1', 'test-vimp_concordance_S4.R:4:1',
    'test-vimp_corelearn_S4.R:7:1', 'test-vimp_correlation_S4.R:4:1',
    'test-vimp_glmnet_S4.R:7:1', 'test-vimp_mutual_information_S4.R:5:1',
    'test-vimp_ranger_S4.R:5:1', 'test-vimp_regression_S4.R:5:1'
  • Testing object updates should be done manually. (1):
    'test-update_object.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-collection_labels.R:6:3'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Ecdat'
  Backtrace:
      ▆
   1. ├─familiar:::test.create_good_data_set(outcome_type = outcome_type) at test-collection_labels.R:6:3
   2. │ └─data.table::data.table(Ecdat::Caschool)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-configuration_file.R:5:1'): (code run outside of `test_that()`) ──
  Error in `..error_package_not_installed(x = missing_packages, purpose = purpose)`: The following package has to be installed to configure familiar using a configuration file: xml2.
  
  Install from CRAN: 
  
  	install.packages(c("xml2"))
  Backtrace:
      ▆
   1. └─familiar:::.load_configuration_file(config) at test-configuration_file.R:5:1
   2.   ├─familiar:::require_package("xml2", "to configure familiar using a configuration file")
   3.   └─familiar:::require_package("xml2", "to configure familiar using a configuration file")
   4.     └─familiar (local) .local(x, ...)
   5.       └─familiar:::.require_package(x = x, purpose = purpose, message_type = message_type)
   6.         └─familiar:::..error_package_not_installed(...)
  ── Error ('test-metric_auc_roc_S4.R:56:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'MASS'
  Backtrace:
      ▆
   1. ├─familiar:::test_all_metrics(...) at test-metric_auc_roc_S4.R:56:1
   2. │ └─familiar:::test.create_good_data_set(outcome_type)
   3. │   └─data.table::as.data.table(MASS::Boston)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-metric_brier_S4.R:56:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'MASS'
  Backtrace:
      ▆
   1. ├─familiar:::test_all_metrics(metrics = familiar:::.get_available_brier_metrics()) at test-metric_brier_S4.R:56:1
   2. │ └─familiar:::test.create_good_data_set(outcome_type)
   3. │   └─data.table::as.data.table(MASS::Boston)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-metric_concordance_index_S4.R:89:1'): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'MASS'
  Backtrace:
      ▆
   1. ├─familiar:::test_all_metrics(...) at test-metric_concordance_index_S4.R:89:1
   2. │ └─familiar:::test.create_good_data_set(outcome_type)
   3. │   └─data.table::as.data.table(MASS::Boston)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-sample_weights.R:2:1'): (code run outside of `test_that()`) ────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'MASS'
  Backtrace:
      ▆
   1. ├─familiar:::test.create_good_data_set(outcome_type = "binomial") at test-sample_weights.R:2:1
   2. │ └─data.table::as.data.table(MASS::biopsy)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-stratification.R:10:3'): (code run outside of `test_that()`) ───
  Error in `.report_missing_package_messages()`: The following package has to be installed to compute similarity using the mutual_information metric: praznik.
  The following package has to be installed to train a novelty detector using the isolation_forest algorithm: isotree.
  The following package has to be installed to train a model for inferring hyperparameter scores: laGP.
  The following package has to be installed to compute p-values for model calibration tests: harmonicmeanp.
  The following packages have to be installed to create plots: ggplot2, labeling, scales and gtable.
  The following packages have to be installed: praznik, isotree, laGP, harmonicmeanp, ggplot2, labeling, scales and gtable.
  
  Install from CRAN: 
  
  	install.packages(c("praznik", "isotree", "laGP", "harmonicmeanp", "ggplot2", "labeling", "scales", "gtable"))
  Backtrace:
      ▆
   1. ├─familiar:::test_train(...) at test-stratification.R:10:3
   2. └─familiar:::test_train(...)
   3.   └─familiar (local) .local(data, ...)
   4.     ├─base::do.call(...)
   5.     └─familiar (local) `<fn>`(...)
   6.       └─familiar:::.report_missing_package_messages()
  ── Error ('test-vimp_table.R:7:1'): (code run outside of `test_that()`) ────────
  Error in `.report_missing_package_messages()`: The following package has to be installed to create clusters faster: fastcluster.
  The following package has to be installed to train a novelty detector using the isolation_forest algorithm: isotree.
  The following package has to be installed to train a model for inferring hyperparameter scores: laGP.
  The following package has to be installed to compute p-values for model calibration tests: harmonicmeanp.
  The following packages have to be installed to create plots: ggplot2, labeling, scales and gtable.
  The following packages have to be installed: fastcluster, isotree, laGP, harmonicmeanp, ggplot2, labeling, scales and gtable.
  
  Install from CRAN: 
  
  	install.packages(c("fastcluster", "isotree", "laGP", "harmonicmeanp", "ggplot2", "labeling", "scales", "gtable"))
  Backtrace:
      ▆
   1. ├─familiar:::prepare_vimp_object(...) at test-vimp_table.R:7:1
   2. └─familiar:::prepare_vimp_object(...)
   3.   └─familiar (local) .local(data, ...)
   4.     ├─base::do.call(...)
   5.     └─familiar (local) `<fn>`(...)
   6.       └─familiar:::.report_missing_package_messages()
  
  [ FAIL 8 | WARN 0 | SKIP 65 | PASS 3551 ]
  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 ... [37s/50s] OK
* checking HTML version of manual ... [34s/50s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/familiar.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 13:22.20, 674.07 + 30.62