Running 'CBDA_test_training.R' [30s]
Running the tests in 'tests/CBDA_test_training.R' failed.
Complete output:
  > # Attach the CBDA library
  > suppressPackageStartupMessages(library(CBDA))
  > suppressPackageStartupMessages(library(randomForest ))
  > suppressPackageStartupMessages(library(glmnet ))
  > suppressPackageStartupMessages(library(SuperLearner))
  > suppressPackageStartupMessages(library(bartMachine))
  > 
  > library(CBDA, quietly = TRUE, verbose = FALSE)
  > CBDA_initialization()
  package missForest already installed
  package stats already installed
  package utils already installed
  package prettydoc already installed
  package foreach already installed
  package SuperLearner already installed
  package knockoff already installed
  package caret already installed
  package smotefamily already installed
  package parallel already installed
  package doParallel already installed
  package glmnet already installed
  Loading required package: prettydoc
  Loading required package: knockoff
  Loading required package: caret
  Loading required package: lattice
  Loading required package: ggplot2
  
  Attaching package: 'ggplot2'
  
  The following object is masked from 'package:randomForest':
  
      margin
  
  Error: package or namespace load failed for 'caret' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info, stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le, stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8, stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii, stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode, stri_endswith, stri_endswith_charclass, stri_endswith_coll, stri_endswith_fixed, stri_escape_unicode, stri_extract, stri_extract_all, stri_extract_all_boundaries, stri_extract_all_charclass, stri_extract_all_coll, stri_extract_all_fixed, stri_extract_all_regex, stri_extract_all_words, stri_extract_first, stri_extract_first_boundaries, stri_extract_first_charclass, stri_extract_first_coll, stri_extract_first_fixed, stri_extract_first_regex, stri_extract_first_words, stri_extract_last, stri_extract_last_boundaries, stri_extract_last_charclass, stri_extract_last_coll, stri_extract_last_fixed, stri_extract_last_regex, stri_extract_last_words, stri_flatten, stri_info, stri_isempty, stri_join, stri_join_list, stri_length, stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list, stri_locale_set, stri_locate, stri_locate_all, stri_locate_all_boundaries, stri_locate_all_charclass, stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex, stri_locate_all_words, stri_locate_first, stri_locate_first_boundaries, stri_locate_first_charclass, stri_locate_first_coll, stri_locate_first_fixed, stri_locate_first_regex, stri_locate_first_words, stri_locate_last, stri_locate_last_boundaries, stri_locate_last_charclass, stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex, stri_locate_last_words, stri_match, stri_match_all, stri_match_all_regex, stri_match_first, stri_match_first_regex, stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes, stri_opts_brkiter, stri_opts_collator, stri_opts_fixed, stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left, stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum, stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw, stri_remove_empty, stri_replace, stri_replace_all, stri_replace_all_charclass, stri_replace_all_coll, stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first, stri_replace_first_charclass, stri_replace_first_coll, stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last, stri_replace_last_charclass, stri_replace_last_coll, stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na, stri_reverse, stri_sort, stri_split, stri_split_boundaries, stri_split_charclass, stri_split_coll, stri_split_fixed, stri_split_lines, stri_split_lines1, stri_split_regex, stri_startswith, stri_startswith_charclass, stri_startswith_coll, stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub, stri_subset, stri_subset_charclass, stri_subset_coll, stri_subset_fixed, stri_subset_regex, stri_timezone_get, stri_timezone_info, stri_timezone_list, stri_timezone_set, stri_trans_char, stri_trans_general, stri_trans_isnfc, stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold, stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd, stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd, stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim, stri_trim_both, stri_trim_left, stri_trim_right, stri_unescape_unicode, stri_unique, stri_width, stri_wrap, stri_write_lines
  Loading required package: smotefamily
  Loading required package: parallel
  Loading required package: doParallel
    missForest        stats        utils    prettydoc      foreach SuperLearner 
          TRUE         TRUE         TRUE         TRUE         TRUE         TRUE 
      knockoff        caret  smotefamily     parallel   doParallel       glmnet 
          TRUE        FALSE         TRUE         TRUE         TRUE         TRUE 
  > 
  > # Set the specs for the synthetic dataset to be tested
  > n = 300          # number of observations
  > p = 100          # number of variables
  > 
  > # Generate a nxp matrix of IID variables (e.g., ~N(0,1))
  > X1 = matrix(rnorm(n*p), nrow=n, ncol=p)
  > 
  > # Setting the nonzero variables - signal variables
  > #nonzero=c(1,100,200,300,400,500,600,700,800,900)
  > nonzero=c(10,20,30,40,50,60,70,80,90,100)
  > 
  > # Set the signal amplitude (for noise level = 1)
  > amplitude = 10
  > 
  > # Allocate the nonzero coefficients in the correct places
  > beta = amplitude * (1:p %in% nonzero)
  > 
  > # Generate a linear model with a bias (e.g., white  noise ~N(0,1))
  > ztemp <- function() X1 %*% beta + rnorm(n)
  > z = ztemp()
  > 
  > # Pass it through an inv-logit function to
  > # generate the Bernoulli response variable Ytemp
  > pr = 1/(1+exp(-z))
  > Ytemp = rbinom(n,1,pr)
  > X2 <- cbind(Ytemp,X1)
  > 
  > dataset_file ="Binomial_dataset.txt"
  > 
  > # Save the synthetic dataset
  > a <- tempdir()
  > write.table(X2, file = file.path(a, dataset_file), sep=",")
  > 
  > # Load the Synthetic dataset
  > #Data = read.csv(paste0(file.path(a),'/',dataset_file),header = TRUE)
  > Data = read.csv(file.path(a, dataset_file),header = TRUE)
  > Ytemp <- Data[,1] # set the outcome
  > original_names_Data <- names(Data)
  > cols_to_eliminate=1
  > Xtemp <- Data[-cols_to_eliminate] # set the matrix X of features/covariates
  > original_names_Xtemp <- names(Xtemp)
  > 
  > # Add more wrappers/algorithms to the SuperLearner ensemble predictor
  > # It can be commented out if only the default set of algorithms are used,
  > # e.g., algorithm_list = c("SL.glm","SL.xgboost","SL.glmnet","SL.svm",
  > #                          "SL.randomForest","SL.bartMachine")
  > # This defines a "new" wrapper, based on the default SL.glmnet
  >  SL.glmnet.0.75 <- function(..., alpha = 0.75,family="binomial"){
  +                   SL.glmnet(..., alpha = alpha, family = family)}
  > 
  > # Using Support Vector Machine and the new Glmnet wrapper above
  >  #test_example <- c("SL.glmnet","SL.glmnet.0.75")
  >  test_example <- c("SL.glmnet","SL.svm","SL.randomForest","SL.bartMachine")
  > 
  >  ## SINGLE CORE EXAMPLE - TRAINING/LEARNING ONLY
  > CBDA_singlecore_training <- CBDA.training(Ytemp , Xtemp , M = 8 ,
  +                                 Nrow_min = 60, Nrow_max = 80,
  +                          top = 6, max_covs = 6 , min_covs = 3,
  +                          algorithm_list = test_example , label = "SINGLE_CORE" ,
  +                          workspace_directory = a)
  Subsampling size =  8 
  
  Case Sampling Range - CSR (%) =  60_80 %
  
  Feature Sampling Range - FSR (%) =  5_15 %
  
  Learning/Training steps initiated successfully !!
  Loading required package: e1071
  Error in namespaceExport(ns, exports) : 
    undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
  Calls: CBDA.training
  Execution halted