Running 'runTests.R' [27s]
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > BiocGenerics:::testPackage("MetaIntegrator")
  Converting probes:genes for gene list for all discovery GEMs...   done. 
  sum weighted AUC: 186.0887 
  worst AUC decrease= -4.443771 
  removing  Gene54 ; new weighted AUC: 190.5325 
  worst AUC decrease= -3.540278 
  removing  Gene56 ; new weighted AUC: 194.0728 
  worst AUC decrease= -2.252524 
  Final gene set AUCs: 
  sum weighted AUC: 192.6766 
  [[1]]
   [1] "Gene27"  "Gene13"  "Gene7"   "Gene26"  "Gene12"  "Gene42"  "Gene2"  
   [8] "Gene17"  "Gene35"  "Gene23"  "Gene158" "Gene19" 
  
  [[2]]
   [1] "Gene62" "Gene63" "Gene50" "Gene59" "Gene66" "Gene45" "Gene49" "Gene47"
   [9] "Gene48" "Gene53"
  
  Used  12 of  12  pos genes, and  12  of  12  neg genes 
  Used  12 of  12  pos genes, and  12  of  12  neg genes 
  Used  12 of  12  pos genes, and  12  of  12  neg genes 
  Used  12 of  12  pos genes, and  12  of  12  neg genes 
  Found common probes in 3 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...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_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
  In addition: Warning messages:
  1: In .metaCheckAll(object, objectStage) : $metaAnalysis is null.
  2: In .metaCheckAll(object, objectStage) : $metaAnalysis is null.
  3: In .metaCheckAll(object, objectStage) : $filterResults is null.
  Error in filterGenes(wrongTinyMetaObject, isLeaveOneOut = FALSE) : 
    Error in the input object!
  In addition: Warning message:
  In .metaCheckAll(object, objectStage) : $metaAnalysis is null.
  Error in filterGenes(wrongTinyMetaObject, isLeaveOneOut = TRUE) : 
    Error in the input object!
  In addition: Warning message:
  In .metaCheckAll(object, objectStage) : $metaAnalysis is null.
  Error in forestPlot(tinyMetaObject, geneName = "12341546576877564534") : 
    No gene named '12341546576877564534' in this metaObject. No plot generated
  [1] "character"
  [1] "character"
  Converting probes:genes for gene list for all discovery GEMs...   done. 
  next best= 250.7598 
  Adding  Gene13 250.7598 
  next best= 6.550584 
  Adding  Gene45 257.3104 
  next best= -3.436114 
  
  Final discovery AUCs from forward search genes:
  Whole Blood Study 1 0.841 
  Whole Blood Study 2 0.779 
  PBMC Study 1 0.917 
  mean AUC: 0.8456667 
  Error in getMostRecentFilter(wrongTinyMetaObject) : 
    Error in the input object!
  In addition: Warning message:
  In .metaCheckAll(object, objectStage) : $filterResults is null.
  Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset Whole Blood Study 1, AUC = 0.856Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset Whole Blood Study 1, AUC = 0.856Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset Whole Blood Study 2, AUC = 0.867Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset Whole Blood Study 2, AUC = 0.867Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset PBMC Study 1, AUC = 0.955Used  12 of  12  pos genes, and  12  of  12  neg genes 
  For dataset PBMC Study 1, AUC = 0.955Found common probes in 3 
  Computing effect sizes...
  Computing summary effect sizes...
  Computing Fisher's output...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_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
  Error in checkTrue(!is(runMetaNoLOOA, "try-error")) : Test not TRUE
  
  Error in summarizeFilterResults(tinyMetaObject, "BIGFAKELABEL") : 
    Error! The input label does not match any filter run
  Error in violinPlot(tinyMetaObject$filterResults$pValueFDR0.05_es0_nStudies1_looaTRUE_hetero0,  : 
    Column named 'fake' not present in the datasetObject$pheno data frame
  
  
  RUNIT TEST PROTOCOL -- Fri Nov 09 04:21:45 2018 
  *********************************************** 
  Number of test functions: 2 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  MetaIntegrator RUnit Tests - 2 test functions, 2 errors, 0 failures
  ERROR in D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_checkDataObject.R: Error while sourcing  D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_checkDataObject.R : 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_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
  ERROR in D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_runMetaAnalysis.R: Error while sourcing  D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_runMetaAnalysis.R : Error in checkTrue(!is(runMetaNoLOOA, "try-error")) : Test not TRUE
  
  
  Test files with failing tests
  
     test_checkDataObject.R 
       D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_checkDataObject.R 
  
     test_runMetaAnalysis.R 
       D:/temp/RtmpWE8TXd/RLIBS_2596c179b775b/MetaIntegrator/unitTests/test_runMetaAnalysis.R 
  
  
  Error in BiocGenerics:::testPackage("MetaIntegrator") : 
    unit tests failed for package MetaIntegrator
  Execution halted