Running ‘testthat.R’ [67s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost", reporter = ProgressReporter)
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | basic                                                           
  ⠏ |   0       | basic functions                                                 
  ⠋ |   1       | basic functions                                                 
  ⠸ |   4       | basic functions                                                 
  ⠧ |   8       | basic functions                                                 [1]	train-rmse:1.678965 
  [2]	train-rmse:1.678965 
  [3]	train-rmse:1.524624 
  [4]	train-rmse:1.441523 
  [5]	train-rmse:1.437758 
  [6]	train-rmse:1.377895 
  [7]	train-rmse:1.305894 
  [8]	train-rmse:1.336120 
  [9]	train-rmse:1.316072 
  [10]	train-rmse:1.316031 
  [11]	train-rmse:1.319404 
  [12]	train-rmse:1.235097 
  [13]	train-rmse:1.225430 
  [14]	train-rmse:1.221079 
  [15]	train-rmse:1.235220 
  [16]	train-rmse:1.219153 
  [17]	train-rmse:1.226439 
  [18]	train-rmse:1.235026 
  [19]	train-rmse:1.244651 
  [20]	train-rmse:1.253197 
  [21]	train-rmse:1.262494 
  [22]	train-rmse:1.272865 
  [23]	train-rmse:1.276073 
  [24]	train-rmse:1.277041 
  [25]	train-rmse:1.287974 
  [26]	train-rmse:1.289816 
  [27]	train-rmse:1.292365 
  [28]	train-rmse:1.282785 
  [29]	train-rmse:1.283805 
  [30]	train-rmse:1.290661 
  [31]	train-rmse:1.289439 
  [32]	train-rmse:1.281995 
  
  ⠙ |  12       | basic functions                                                 
  ⠴ |  26       | basic functions                                                 [1]	train-error:0.027944 
  
  ⠙ |  32       | basic functions                                                 
  ⠴ |  36       | basic functions                                                 
  ⠋ |  41       | basic functions                                                 
  ⠼ |  45       | basic functions                                                 [1]	train-error:0.000614 
  [2]	train-error:0.001228 
  [3]	train-error:0.000614 
  [4]	train-error:0.000614 
  
  ⠹ |  53       | basic functions                                                 
  ⠸ |  54       | basic functions                                                 [1]	train-error:0.046522+0.000800	test-error:0.046524+0.003197 
  [2]	train-error:0.022263+0.000612	test-error:0.022265+0.002444 
  [1]	train-error:0.046522+0.000814	test-error:0.046523+0.003254 
  [2]	train-error:0.022263+0.000797	test-error:0.022264+0.003190 
  
  ⠼ |  65       | basic functions                                                 
  ⠴ |  66       | basic functions                                                 
  ⠦ |  67       | basic functions                                                 
  ⠋ |  71       | basic functions                                                 [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  
  ⠴ |  76       | basic functions                                                 
  ⠧ |  78       | basic functions                                                 [1]	train-error:0.046522	train-auc:0.958228	train-logloss:0.233366 
  [2]	train-error:0.022263	train-auc:0.981413	train-logloss:0.136656 
  
  ✔ |  79       | basic functions [14.8 s]
  
  ⠏ |   0       | callbacks                                                       
  ⠏ |   0       | callbacks                                                       
  ⠋ |   1       | callbacks                                                       [1]	train-auc:0.900000	test-auc:0.800000 
  
  ⠸ |  24       | callbacks                                                       
  ⠴ |  26       | callbacks                                                       
  ⠏ |  30       | callbacks                                                       
  ⠸ |  34       | callbacks                                                       
  ⠧ |  38       | callbacks                                                       
  ⠏ |  40       | callbacks                                                       
  ⠹ |  43       | callbacks                                                       
  ⠇ |  48   1   | callbacks                                                       
  ⠙ |  51   1   | callbacks                                                       
  ⠧ |  57   1   | callbacks                                                       
  ⠹ |  62   1   | callbacks                                                       
  ⠇ |  68   1   | callbacks                                                       
  ⠸ |  73   1   | callbacks                                                       
  ⠧ |  77   1   | callbacks                                                       
  ⠋ |  80   1   | callbacks                                                       
  ⠸ |  83   1   | callbacks                                                       
  ⠙ |  91   1   | callbacks                                                       
  ✔ |  94   1   | callbacks [8.6 s]
  ────────────────────────────────────────────────────────────────────────────────
  Warning (test_callbacks.R:193:3): cb.save.model works as expected
  one argument not used by format 'xgboost.model'
  Backtrace:
   1. xgboost::xgb.train(...) test_callbacks.R:193:2
   2. xgboost:::f()
   4. base::sprintf(save_name, env$iteration)
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | custom_objective                                                
  ⠏ |   0       | Test models with custom objective                               [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  
  ⠋ |   1       | Test models with custom objective                               
  ⠼ |   5       | Test models with custom objective                               [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [3]	eval-error:0.018001	train-error:0.015200 
  [4]	eval-error:0.018001	train-error:0.015200 
  [5]	eval-error:0.006207	train-error:0.007063 
  [6]	eval-error:0.000000	train-error:0.001228 
  [7]	eval-error:0.000000	train-error:0.001228 
  [8]	eval-error:0.000000	train-error:0.001228 
  [9]	eval-error:0.000000	train-error:0.001228 
  [10]	eval-error:0.000000	train-error:0.000000 
  
  ⠧ |   8       | Test models with custom objective                               [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  
  ✔ |  12   1   | Test models with custom objective [0.7 s]
  ────────────────────────────────────────────────────────────────────────────────
  Warning (test_custom_objective.R:50:3): custom objective with early stop works
  coercing argument of type 'double' to logical
  Backtrace:
   1. testthat::expect_true(all(diff(train_log)) <= 0) test_custom_objective.R:50:2
   2. testthat::quasi_label(enquo(object), label, arg = "object")
   3. rlang::eval_bare(expr, quo_get_env(quo))
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | dmatrix                                                         
  ⠏ |   0       | testing xgb.DMatrix functionality                               
  ⠧ |   8       | testing xgb.DMatrix functionality                               
  ⠙ |  22       | testing xgb.DMatrix functionality                               
  ⠇ |  29       | testing xgb.DMatrix functionality                               
  ✔ |  37       | testing xgb.DMatrix functionality [0.4 s]
  
  ⠏ |   0       | gc_safety                                                       
  ⠏ |   0       | Garbage Collection Safety Check                                 [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  
  ⠋ |   0     1 | Garbage Collection Safety Check                                 
  ✔ |   0     1 | Garbage Collection Safety Check [28.4 s]
  ────────────────────────────────────────────────────────────────────────────────
  Skip (test_gc_safety.R:5:1): train and prediction when gctorture is on
  Reason: empty test
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | glm                                                             
  ⠏ |   0       | Test generalized linear models                                  
  ⠴ |   6       | Test generalized linear models                                  
  ⠧ |   8       | Test generalized linear models                                  
  ✔ |  11       | Test generalized linear models [0.4 s]
  
  ⠏ |   0       | helpers                                                         
  ⠏ |   0       | Test helper functions                                           
  ⠋ |   1       | Test helper functions                                           [1]	train-error:0.333333 
  [1]	train-rmse:1.940066 
  [2]	train-rmse:1.560864 
  [3]	train-rmse:1.277414 
  [4]	train-rmse:1.068562 
  [5]	train-rmse:0.903897 
  [6]	train-rmse:0.763228 
  [7]	train-rmse:0.664924 
  [8]	train-rmse:0.570358 
  [9]	train-rmse:0.507416 
  [10]	train-rmse:0.458599 
  [11]	train-rmse:0.394349 
  [12]	train-rmse:0.355794 
  [13]	train-rmse:0.305484 
  [14]	train-rmse:0.271176 
  [15]	train-rmse:0.259943 
  [16]	train-rmse:0.238429 
  [17]	train-rmse:0.228003 
  [18]	train-rmse:0.212117 
  [19]	train-rmse:0.187830 
  [20]	train-rmse:0.173381 
  [21]	train-rmse:0.164001 
  [22]	train-rmse:0.156113 
  [23]	train-rmse:0.143242 
  [24]	train-rmse:0.130215 
  [25]	train-rmse:0.120160 
  [26]	train-rmse:0.112119 
  [27]	train-rmse:0.104753 
  [28]	train-rmse:0.096786 
  [29]	train-rmse:0.089361 
  [30]	train-rmse:0.083706 
  
  ⠧ |  48       | Test helper functions                                           
  ⠦ | 167       | Test helper functions                                           [1]	train-rmse:1.940066 
  [2]	train-rmse:1.675038 
  [3]	train-rmse:1.462383 
  [4]	train-rmse:1.283198 
  [5]	train-rmse:1.155542 
  [6]	train-rmse:1.049559 
  [7]	train-rmse:0.942910 
  [8]	train-rmse:0.859371 
  [9]	train-rmse:0.774970 
  [10]	train-rmse:0.725452 
  [11]	train-rmse:0.679127 
  [12]	train-rmse:0.628614 
  [13]	train-rmse:0.594549 
  [14]	train-rmse:0.535545 
  [15]	train-rmse:0.485623 
  [16]	train-rmse:0.460187 
  [17]	train-rmse:0.413632 
  [18]	train-rmse:0.403692 
  [19]	train-rmse:0.385314 
  [20]	train-rmse:0.366654 
  [21]	train-rmse:0.354532 
  [22]	train-rmse:0.326526 
  [23]	train-rmse:0.316875 
  [24]	train-rmse:0.301910 
  [25]	train-rmse:0.285458 
  [26]	train-rmse:0.275437 
  [27]	train-rmse:0.267556 
  [28]	train-rmse:0.263727 
  [29]	train-rmse:0.253460 
  [30]	train-rmse:0.235433 
  
  ⠏ | 250       | Test helper functions                                           
  ⠦ | 357       | Test helper functions                                           
  ⠏ | 440       | Test helper functions                                           
  ⠼ | 495       | Test helper functions                                           
  ⠙ | 562       | Test helper functions                                           
  ⠏ | 620       | Test helper functions                                           
  ⠴ | 666       | Test helper functions                                           
  ⠼ | 675       | Test helper functions                                           
  ⠸ | 684       | Test helper functions                                           
  ⠴ | 686       | Test helper functions                                           
  ⠦ | 696     1 | Test helper functions                                           
  ⠧ | 697     1 | Test helper functions                                           
  ⠇ | 698     1 | Test helper functions                                           
  ✔ | 705     1 | Test helper functions [4.5 s]
  ────────────────────────────────────────────────────────────────────────────────
  Skip (test_helpers.R:337:1): xgb.plot.tree works with and without feature names
  Reason: empty test
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | interaction_constraints                                         
  ⠏ |   0       | interaction constraints                                         
  ⠋ |   1       | interaction constraints                                         
  ⠙ |   2       | interaction constraints                                         
  ✔ |   2       | interaction constraints [6.9 s]
  
  ⠏ |   0       | interactions                                                    
  ⠏ |   0       | Test prediction of feature interactions                         
  ⠋ |   1       | Test prediction of feature interactions                         
  ⠸ |   4       | Test prediction of feature interactions                         
  ⠼ |  15       | Test prediction of feature interactions                         
  ✔ |  17       | Test prediction of feature interactions [1.3 s]
  
  ⠏ |   0       | model_compatibility                                             
  ⠏ |   0       | Models from previous versions of XGBoost can be loaded          trying URL 'https://xgboost-ci-jenkins-artifacts.s3-us-west-2.amazonaws.com/xgboost_r_model_compatibility_test.zip'
  Content type 'application/zip' length 77308 bytes (75 KB)
  ==================================================
  downloaded 75 KB
  
  [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  
  ⠋ |   1       | Models from previous versions of XGBoost can be loaded          [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  [17:56:51] WARNING: amalgamation/../src/learner.cc:764: Loading model from XGBoost < 1.0.0, consider saving it again for improved compatibility
  
  ⠼ |  21   4   | Models from previous versions of XGBoost can be loaded          
  ✖ |  22 1 4   | Models from previous versions of XGBoost can be loaded [1.4 s]
  ────────────────────────────────────────────────────────────────────────────────
  Warning (test_model_compatibility.R:69:3): Models from previous versions of XGBoost can be loaded
  The model had been generated by XGBoost version 1.0.0 or earlier and was loaded from a RDS file. We strongly ADVISE AGAINST using saveRDS() function, to ensure that your model can be read in current and upcoming XGBoost releases. Please use xgb.save() instead to preserve models for the long term. For more details and explanation, see https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
  Backtrace:
    1. base::lapply(...) test_model_compatibility.R:69:2
    2. xgboost:::FUN(X[[i]], ...)
    4. xgboost:::predict.xgb.Booster(booster, newdata = pred_data)
    5. xgboost::xgb.Booster.complete(object, saveraw = FALSE)
    6. xgboost:::xgb.Booster.handle(modelfile = object$raw)
    7. xgboost::xgb.unserialize(modelfile)
    8. base::tryCatch(...)
    9. base:::tryCatchList(expr, classes, parentenv, handlers)
   10. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. value[[3L]](cond)
  
  Warning (test_model_compatibility.R:69:3): Models from previous versions of XGBoost can be loaded
  The model had been generated by XGBoost version 1.0.0 or earlier and was loaded from a RDS file. We strongly ADVISE AGAINST using saveRDS() function, to ensure that your model can be read in current and upcoming XGBoost releases. Please use xgb.save() instead to preserve models for the long term. For more details and explanation, see https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
  Backtrace:
    1. base::lapply(...) test_model_compatibility.R:69:2
    2. xgboost:::FUN(X[[i]], ...)
    3. xgboost:::run_booster_check(booster, name) test_model_compatibility.R:82:4
    4. xgboost::xgb.Booster.complete(booster) test_model_compatibility.R:31:4
    5. xgboost:::xgb.Booster.handle(modelfile = object$raw)
    6. xgboost::xgb.unserialize(modelfile)
    7. base::tryCatch(...)
    8. base:::tryCatchList(expr, classes, parentenv, handlers)
    9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. value[[3L]](cond)
  
  Warning (test_model_compatibility.R:69:3): Models from previous versions of XGBoost can be loaded
  The model had been generated by XGBoost version 1.0.0 or earlier and was loaded from a RDS file. We strongly ADVISE AGAINST using saveRDS() function, to ensure that your model can be read in current and upcoming XGBoost releases. Please use xgb.save() instead to preserve models for the long term. For more details and explanation, see https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
  Backtrace:
    1. base::lapply(...) test_model_compatibility.R:69:2
    2. xgboost:::FUN(X[[i]], ...)
    4. xgboost:::predict.xgb.Booster(booster, newdata = pred_data)
    5. xgboost::xgb.Booster.complete(object, saveraw = FALSE)
    6. xgboost:::xgb.Booster.handle(modelfile = object$raw)
    7. xgboost::xgb.unserialize(modelfile)
    8. base::tryCatch(...)
    9. base:::tryCatchList(expr, classes, parentenv, handlers)
   10. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. value[[3L]](cond)
  
  Warning (test_model_compatibility.R:69:3): Models from previous versions of XGBoost can be loaded
  The model had been generated by XGBoost version 1.0.0 or earlier and was loaded from a RDS file. We strongly ADVISE AGAINST using saveRDS() function, to ensure that your model can be read in current and upcoming XGBoost releases. Please use xgb.save() instead to preserve models for the long term. For more details and explanation, see https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
  Backtrace:
    1. base::lapply(...) test_model_compatibility.R:69:2
    2. xgboost:::FUN(X[[i]], ...)
    3. xgboost:::run_booster_check(booster, name) test_model_compatibility.R:82:4
    4. xgboost::xgb.Booster.complete(booster) test_model_compatibility.R:31:4
    5. xgboost:::xgb.Booster.handle(modelfile = object$raw)
    6. xgboost::xgb.unserialize(modelfile)
    7. base::tryCatch(...)
    8. base:::tryCatchList(expr, classes, parentenv, handlers)
    9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. value[[3L]](cond)
  
  Error (test_model_compatibility.R:69:3): Models from previous versions of XGBoost can be loaded
  Error: [17:56:51] amalgamation/../src/objective/./regression_loss.h:89: Check failed: base_score > 0.0f && base_score < 1.0f: base_score must be in (0,1) for logistic loss, got: -0
  Stack trace:
    [bt] (0) /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/xgboost/libs/xgboost.so(dmlc::LogMessageFatal::~LogMessageFatal()+0x5f) [0x7f84f2a84a9f]
    [bt] (1) /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/xgboost/libs/xgboost.so(xgboost::obj::LogisticRegression::ProbToMargin(float)+0xbf) [0x7f84f2b10acf]
    [bt] (2) /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/xgboost/libs/xgboost.so(xgboost::LearnerIO::LoadModel(dmlc::Stream*)+0x9c0) [0x7f84f2b9d100]
    [bt] (3) /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/xgboost/libs/xgboost.so(XGBoosterLoadModel+0x233) [0x7f84f2aa11c3]
    [bt] (4) /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/xgboost/libs/xgboost.so(XGBoosterLoadModel_R+0x38) [0x7f84f2a80e88]
    [bt] (5) /home/hornik/tmp/R.check/r-devel-gcc/Work/b
  Backtrace:
   1. base::lapply(...) test_model_compatibility.R:69:2
   2. xgboost:::FUN(X[[i]], ...)
   3. xgboost::xgb.load(model_file) test_model_compatibility.R:79:6
   4. xgboost:::xgb.Booster.handle(modelfile = modelfile)
  ────────────────────────────────────────────────────────────────────────────────
  
  ⠏ |   0       | monotone                                                        
  ⠏ |   0       | monotone constraints                                            
  ✔ |   1       | monotone constraints
  
  ⠏ |   0       | parameter_exposure                                              
  ⠏ |   0       | Test model params and call are exposed to R                     
  ✔ |   6       | Test model params and call are exposed to R
  
  ⠏ |   0       | poisson_regression                                              
  ⠏ |   0       | Test poisson regression model                                   
  ✔ |   3       | Test poisson regression model
  
  ⠏ |   0       | ranking                                                         
  ⠏ |   0       | Learning to rank                                                [1]	train-auc:0.625000	train-aucpr:0.550000 
  [2]	train-auc:0.750000	train-aucpr:0.700000 
  [3]	train-auc:0.875000	train-aucpr:0.850000 
  [4]	train-auc:1.000000	train-aucpr:1.000000 
  [5]	train-auc:1.000000	train-aucpr:1.000000 
  [6]	train-auc:1.000000	train-aucpr:1.000000 
  [7]	train-auc:1.000000	train-aucpr:1.000000 
  [8]	train-auc:1.000000	train-aucpr:1.000000 
  [9]	train-auc:1.000000	train-aucpr:1.000000 
  [10]	train-auc:1.000000	train-aucpr:1.000000 
  [1]	train-auc:0.625000	train-aucpr:0.550000 
  [2]	train-auc:0.750000	train-aucpr:0.700000 
  [3]	train-auc:0.875000	train-aucpr:0.850000 
  [4]	train-auc:0.875000	train-aucpr:0.850000 
  [5]	train-auc:0.875000	train-aucpr:0.850000 
  [6]	train-auc:0.875000	train-aucpr:0.850000 
  [7]	train-auc:0.875000	train-aucpr:0.850000 
  [8]	train-auc:1.000000	train-aucpr:1.000000 
  [9]	train-auc:1.000000	train-aucpr:1.000000 
  [10]	train-auc:1.000000	train-aucpr:1.000000 
  
  ✔ |  14       | Learning to rank
  
  ⠏ |   0       | update                                                          
  ⠏ |   0       | update trees in an existing model                               [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  
  ⠋ |   1       | update trees in an existing model                               [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  
  ⠦ |   7       | update trees in an existing model                               [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  
  ⠼ |  15       | update trees in an existing model                               [17:56:52] WARNING: amalgamation/../src/gbm/gbtree.cc:73: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using`tree_method` parameter instead.
  
  ✔ |  22       | update trees in an existing model [0.5 s]
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  Duration: 68.1 s
  
  ── Skipped tests  ──────────────────────────────────────────────────────────────
  ● empty test (2)
  
  [ FAIL 1 | WARN 6 | SKIP 2 | PASS 1025 ]
  Error: Test failures
  Execution halted