Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lilikoi)
  > 
  > test_check("lilikoi")
  [1] "18 out of 19 Matched metabolites 100 %"
  [1] "1 out of 19 UnMatched metabolites 0 %"
  robust_score_bydist. min_exp= 0 , min_std= 0 
  skipping pathway  1  k1= 0 
  skipping pathway  2  k1= 0 
  skipping pathway  3  k1= 0 
  skipping pathway  4  k1= 0 
  skipping pathway  5  k1= 0 
  skipping pathway  6  k1= 0 
  skipping pathway  7  k1= 0 
  skipping pathway  8  k1= 0 
  skipping pathway  9  k1= 0 
  skipping pathway  10  k1= 0 
  skipping pathway  11  k1= 0 
  skipping pathway  12  k1= 0 
  skipping pathway  13  k1= 0 
  skipping pathway  14  k1= 0 
  skipping pathway  15  k1= 0 
  skipping pathway  16  k1= 0 
  skipping pathway  17  k1= 0 
  skipping pathway  18  k1= 0 
  skipping pathway  19  k1= 0 
  skipping pathway  20  k1= 0 
  skipping pathway  21  k1= 0 
  skipping pathway  22  k1= 0 
  skipping pathway  23  k1= 0 
  skipping pathway  24  k1= 0 
  skipping pathway  25  k1= 0 
  skipping pathway  26  k1= 0 
  skipping pathway  27  k1= 0 
  skipping pathway  28  k1= 0 
  skipping pathway  29  k1= 0 
  skipping pathway  30  k1= 0 
  skipping pathway  31  k1= 0 
  skipping pathway  32  k1= 0 
  skipping pathway  33  k1= 0 
  skipping pathway  34  k1= 0 
  skipping pathway  35  k1= 0 
  skipping pathway  36  k1= 0 
  skipping pathway  37  k1= 0 
  skipping pathway  38  k1= 0 
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  pathway  39 > sig: 0.01154725 
  skipping pathway  40  k1= 0 
  skipping pathway  41  k1= 0 
  skipping pathway  42  k1= 0 
  skipping pathway  43  k1= 0 
  skipping pathway  44  k1= 0 
  skipping pathway  45  k1= 0 
  skipping pathway  46  k1= 0 
  skipping pathway  47  k1= 0 
  skipping pathway  48  k1= 0 
  skipping pathway  49  k1= 0 
  skipping pathway  50  k1= 0 
  skipping pathway  51  k1= 0 
  skipping pathway  52  k1= 0 
  skipping pathway  53  k1= 0 
  skipping pathway  54  k1= 0 
  skipping pathway  55  k1= 0 
  skipping pathway  56  k1= 0 
  skipping pathway  57  k1= 0 
  skipping pathway  58  k1= 0 
  skipping pathway  59  k1= 0 
  skipping pathway  60  k1= 0 
  skipping pathway  61  k1= 0 
  skipping pathway  62  k1= 0 
  skipping pathway  63  k1= 0 
  skipping pathway  64  k1= 0 
  skipping pathway  65  k1= 0 
  skipping pathway  66  k1= 0 
  skipping pathway  67  k1= 0 
  skipping pathway  68  k1= 0 
  skipping pathway  69  k1= 0 
  skipping pathway  70  k1= 0 
  skipping pathway  71  k1= 0 
  skipping pathway  72  k1= 0 
  skipping pathway  73  k1= 0 
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  [1] 1
  pathway  74 > sig: 0.01985462 
  skipping pathway  75  k1= 0 
  skipping pathway  76  k1= 0 
  skipping pathway  77  k1= 0 
  skipping pathway  78  k1= 0 
  skipping pathway  79  k1= 0 
  skipping pathway  80  k1= 0 
  skipping pathway  81  k1= 0 
  skipping pathway  82  k1= 0 
  skipping pathway  83  k1= 0 
  skipping pathway  84  k1= 0 
  skipping pathway  85  k1= 0 
  skipping pathway  86  k1= 0 
  skipping pathway  87  k1= 0 
  skipping pathway  88  k1= 0 
  skipping pathway  89  k1= 0 
  skipping pathway  90  k1= 0 
  skipping pathway  91  k1= 0 
  skipping pathway  92  k1= 0 
  skipping pathway  93  k1= 0 
  skipping pathway  94  k1= 0 
  skipping pathway  95  k1= 0 
  skipping pathway  96  k1= 0 
  skipping pathway  97  k1= 0 
  skipping pathway  98  k1= 0 
  skipping pathway  99  k1= 0 
  skipping pathway  100  k1= 0 
  skipping pathway  101  k1= 0 
  skipping pathway  102  k1= 0 
  skipping pathway  103  k1= 0 
  skipping pathway  104  k1= 0 
  skipping pathway  105  k1= 0 
  skipping pathway  106  k1= 0 
  skipping pathway  107  k1= 0 
  skipping pathway  108  k1= 0 
  skipping pathway  109  k1= 0 
  skipping pathway  110  k1= 0 
  skipping pathway  111  k1= 0 
  skipping pathway  112  k1= 0 
  skipping pathway  113  k1= 0 
  skipping pathway  114  k1= 0 
  skipping pathway  115  k1= 0 
  skipping pathway  116  k1= 0 
  skipping pathway  117  k1= 0 
  skipping pathway  118  k1= 0 
  skipping pathway  119  k1= 0 
  skipping pathway  120  k1= 0 
  skipping pathway  121  k1= 0 
  skipping pathway  122  k1= 0 
  skipping pathway  123  k1= 0 
  skipping pathway  124  k1= 0 
  skipping pathway  125  k1= 0 
  skipping pathway  126  k1= 0 
  skipping pathway  127  k1= 0 
  skipping pathway  128  k1= 0 
  skipping pathway  129  k1= 0 
  skipping pathway  130  k1= 0 
  skipping pathway  131  k1= 0 
  skipping pathway  132  k1= 0 
  skipping pathway  133  k1= 0 
  skipping pathway  134  k1= 0 
  skipping pathway  135  k1= 0 
  skipping pathway  136  k1= 0 
  skipping pathway  137  k1= 0 
  skipping pathway  138  k1= 0 
  skipping pathway  139  k1= 0 
  skipping pathway  140  k1= 0 
  skipping pathway  141  k1= 0 
  skipping pathway  142  k1= 0 
  skipping pathway  143  k1= 0 
  skipping pathway  144  k1= 0 
  skipping pathway  145  k1= 0 
  skipping pathway  146  k1= 0 
  skipping pathway  147  k1= 0 
  skipping pathway  148  k1= 0 
  skipping pathway  149  k1= 0 
  skipping pathway  150  k1= 0 
  skipping pathway  151  k1= 0 
  skipping pathway  152  k1= 0 
  skipping pathway  153  k1= 0 
  skipping pathway  154  k1= 0 
  skipping pathway  155  k1= 0 
  skipping pathway  156  k1= 0 
  skipping pathway  157  k1= 0 
  skipping pathway  158  k1= 0 
  skipping pathway  159  k1= 0 
  skipping pathway  160  k1= 0 
  skipping pathway  161  k1= 0 
  skipping pathway  162  k1= 0 
  skipping pathway  163  k1= 0 
  skipping pathway  164  k1= 0 
  skipping pathway  165  k1= 0 
  skipping pathway  166  k1= 0 
  skipping pathway  167  k1= 0 
  skipping pathway  168  k1= 0 
  skipping pathway  169  k1= 0 
  skipping pathway  170  k1= 0 
  skipping pathway  171  k1= 0 
  skipping pathway  172  k1= 0 
  skipping pathway  173  k1= 0 
  skipping pathway  174  k1= 0 
  skipping pathway  175  k1= 0 
  skipping pathway  176  k1= 0 
  skipping pathway  177  k1= 0 
  skipping pathway  178  k1= 0 
  skipping pathway  179  k1= 0 
  skipping pathway  180  k1= 0 
  skipping pathway  181  k1= 0 
  skipping pathway  182  k1= 0 
  skipping pathway  183  k1= 0 
  skipping pathway  184  k1= 0 
  skipping pathway  185  k1= 0 
  skipping pathway  186  k1= 0 
  skipping pathway  187  k1= 0 
  skipping pathway  188  k1= 0 
  skipping pathway  189  k1= 0 
  skipping pathway  190  k1= 0 
  skipping pathway  191  k1= 0 
  skipping pathway  192  k1= 0 
  skipping pathway  193  k1= 0 
  skipping pathway  194  k1= 0 
  skipping pathway  195  k1= 0 
  skipping pathway  196  k1= 0 
  skipping pathway  197  k1= 0 
  skipping pathway  198  k1= 0 
  skipping pathway  199  k1= 0 
  skipping pathway  200  k1= 0 
  skipping pathway  201  k1= 0 
  skipping pathway  202  k1= 0 
  skipping pathway  203  k1= 0 
  skipping pathway  204  k1= 0 
  skipping pathway  205  k1= 0 
  skipping pathway  206  k1= 0 
  skipping pathway  207  k1= 0 
  skipping pathway  208  k1= 0 
  skipping pathway  209  k1= 0 
  skipping pathway  210  k1= 0 
  skipping pathway  211  k1= 0 
  skipping pathway  212  k1= 0 
  skipping pathway  213  k1= 0 
  skipping pathway  214  k1= 0 
  skipping pathway  215  k1= 0 
  skipping pathway  216  k1= 0 
  skipping pathway  217  k1= 0 
  skipping pathway  218  k1= 0 
  skipping pathway  219  k1= 0 
  skipping pathway  220  k1= 0 
  skipping pathway  221  k1= 0 
  skipping pathway  222  k1= 0 
  skipping pathway  223  k1= 0 
  skipping pathway  224  k1= 0 
  skipping pathway  225  k1= 0 
  skipping pathway  226  k1= 0 
  skipping pathway  227  k1= 0 
  skipping pathway  228  k1= 0 
  skipping pathway  229  k1= 0 
  skipping pathway  230  k1= 0 
  skipping pathway  231  k1= 0 
  skipping pathway  232  k1= 0 
  skipping pathway  233  k1= 0 
  skipping pathway  234  k1= 0 
  skipping pathway  235  k1= 0 
  skipping pathway  236  k1= 0 
  skipping pathway  237  k1= 0 
  skipping pathway  238  k1= 0 
  skipping pathway  239  k1= 0 
  skipping pathway  240  k1= 0 
  skipping pathway  241  k1= 0 
  skipping pathway  242  k1= 0 
  skipping pathway  243  k1= 0 
  skipping pathway  244  k1= 0 
  skipping pathway  245  k1= 0 
  skipping pathway  246  k1= 0 
  skipping pathway  247  k1= 0 
  skipping pathway  248  k1= 0 
  skipping pathway  249  k1= 0 
  skipping pathway  250  k1= 0 
  skipping pathway  251  k1= 0 
  skipping pathway  252  k1= 0 
  skipping pathway  253  k1= 0 
  skipping pathway  254  k1= 0 
  skipping pathway  255  k1= 0 
  skipping pathway  256  k1= 0 
  skipping pathway  257  k1= 0 
  skipping pathway  258  k1= 0 
  skipping pathway  259  k1= 0 
  skipping pathway  260  k1= 0 
  skipping pathway  261  k1= 0 
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  skipping pathway  263  k1= 0 
  skipping pathway  264  k1= 0 
  skipping pathway  265  k1= 0 
  skipping pathway  266  k1= 0 
  skipping pathway  267  k1= 0 
  skipping pathway  268  k1= 0 
  skipping pathway  269  k1= 0 
  skipping pathway  270  k1= 0 
  skipping pathway  271  k1= 0 
  skipping pathway  272  k1= 0 
  skipping pathway  273  k1= 0 
  skipping pathway  274  k1= 0 
  skipping pathway  275  k1= 0 
  skipping pathway  276  k1= 0 
  skipping pathway  277  k1= 0 
  skipping pathway  278  k1= 0 
  skipping pathway  279  k1= 0 
  skipping pathway  280  k1= 0 
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  skipping pathway  285  k1= 0 
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  skipping pathway  294  k1= 0 
  skipping pathway  295  k1= 0 
  skipping pathway  296  k1= 0 
  skipping pathway  297  k1= 0 
  skipping pathway  298  k1= 0 
  skipping pathway  299  k1= 0 
  skipping pathway  300  k1= 0 
  skipping pathway  301  k1= 0 
  skipping pathway  302  k1= 0 
  skipping pathway  303  k1= 0 
  skipping pathway  304  k1= 0 
  skipping pathway  305  k1= 0 
  skipping pathway  306  k1= 0 
  skipping pathway  307  k1= 0 
  skipping pathway  308  k1= 0 
  skipping pathway  309  k1= 0 
  skipping pathway  310  k1= 0 
  skipping pathway  311  k1= 0 
  skipping pathway  312  k1= 0 
  skipping pathway  313  k1= 0 
  skipping pathway  314  k1= 0 
  skipping pathway  315  k1= 0 
  skipping pathway  316  k1= 0 
  skipping pathway  317  k1= 0 
  skipping pathway  318  k1= 0 
  skipping pathway  319  k1= 0 
  skipping pathway  320  k1= 0 
  skipping pathway  321  k1= 0 
  skipping pathway  322  k1= 0 
  skipping pathway  323  k1= 0 
  skipping pathway  324  k1= 0 
  skipping pathway  325  k1= 0 
  skipping pathway  326  k1= 0 
  skipping pathway  327  k1= 0 
  skipping pathway  328  k1= 0 
  skipping pathway  329  k1= 0 
  skipping pathway  330  k1= 0 
  skipping pathway  331  k1= 0 
  skipping pathway  332  k1= 0 
  skipping pathway  333  k1= 0 
  skipping pathway  334  k1= 0 
  skipping pathway  335  k1= 0 
  skipping pathway  336  k1= 0 
  skipping pathway  337  k1= 0 
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  skipping pathway  350  k1= 0 
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  skipping pathway  352  k1= 0 
  skipping pathway  353  k1= 0 
  skipping pathway  354  k1= 0 
  skipping pathway  355  k1= 0 
  skipping pathway  356  k1= 0 
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  skipping pathway  362  k1= 0 
  skipping pathway  363  k1= 0 
  skipping pathway  364  k1= 0 
  skipping pathway  365  k1= 0 
  skipping pathway  366  k1= 0 
  skipping pathway  367  k1= 0 
  skipping pathway  368  k1= 0 
  skipping pathway  369  k1= 0 
  skipping pathway  370  k1= 0 
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  skipping pathway  372  k1= 0 
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  skipping pathway  390  k1= 0 
  skipping pathway  391  k1= 0 
  skipping pathway  392  k1= 0 
  skipping pathway  393  k1= 0 
  skipping pathway  394  k1= 0 
  skipping pathway  395  k1= 0 
  skipping pathway  396  k1= 0 
  skipping pathway  397  k1= 0 
  skipping pathway  398  k1= 0 
  skipping pathway  399  k1= 0 
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  skipping pathway  611  k1= 0 
  skipping pathway  612  k1= 0 
  skipping pathway  613  k1= 0 
  skipping pathway  614  k1= 0 
  skipping pathway  615  k1= 0 
  skipping pathway  616  k1= 0 
  skipping pathway  617  k1= 0 
  skipping pathway  618  k1= 0 
  skipping pathway  619  k1= 0 
  skipping pathway  620  k1= 0 
  skipping pathway  621  k1= 0 
  skipping pathway  622  k1= 0 
  skipping pathway  623  k1= 0 
  skipping pathway  624  k1= 0 
  skipping pathway  625  k1= 0 
  skipping pathway  626  k1= 0 
  skipping pathway  627  k1= 0 
  skipping pathway  628  k1= 0 
  skipping pathway  629  k1= 0 
  skipping pathway  630  k1= 0 
  skipping pathway  631  k1= 0 
  skipping pathway  632  k1= 0 
  skipping pathway  633  k1= 0 
  skipping pathway  634  k1= 0 
  skipping pathway  635  k1= 0 
  skipping pathway  636  k1= 0 
  skipping pathway  637  k1= 0 
  skipping pathway  638  k1= 0 
  skipping pathway  639  k1= 0 
  skipping pathway  640  k1= 0 
  skipping pathway  641  k1= 0 
  skipping pathway  642  k1= 0 
  skipping pathway  643  k1= 0 
  skipping pathway  644  k1= 0 
  skipping pathway  645  k1= 0 
  skipping pathway  646  k1= 0 
  skipping pathway  647  k1= 0 
  skipping pathway  648  k1= 0 
  skipping pathway  649  k1= 0 
  skipping pathway  650  k1= 0 
  skipping pathway  651  k1= 0 
  skipping pathway  652  k1= 0 
  skipping pathway  653  k1= 0 
  skipping pathway  654  k1= 0 
  skipping pathway  655  k1= 0 
  skipping pathway  656  k1= 0 
  skipping pathway  657  k1= 0 
  skipping pathway  658  k1= 0 
  skipping pathway  659  k1= 0 
  skipping pathway  660  k1= 0 
  skipping pathway  661  k1= 0 
  skipping pathway  662  k1= 0 
  skipping pathway  663  k1= 0 
  skipping pathway  664  k1= 0 
  skipping pathway  665  k1= 0 
  skipping pathway  666  k1= 0 
  skipping pathway  667  k1= 0 
  skipping pathway  668  k1= 0 
  skipping pathway  669  k1= 0 
  skipping pathway  670  k1= 0 
  skipping pathway  671  k1= 0 
  skipping pathway  672  k1= 0 
  skipping pathway  673  k1= 0 
  skipping pathway  674  k1= 0 
  skipping pathway  675  k1= 0 
  skipping pathway  676  k1= 0 
  skipping pathway  677  k1= 0 
  skipping pathway  678  k1= 0 
  skipping pathway  679  k1= 0 
  skipping pathway  680  k1= 0 
  skipping pathway  681  k1= 0 
  skipping pathway  682  k1= 0 
  skipping pathway  683  k1= 0 
  skipping pathway  684  k1= 0 
  skipping pathway  685  k1= 0 
  skipping pathway  686  k1= 0 
  skipping pathway  687  k1= 0 
  skipping pathway  688  k1= 0 
  skipping pathway  689  k1= 0 
  skipping pathway  690  k1= 0 
  skipping pathway  691  k1= 0 
  skipping pathway  692  k1= 0 
  skipping pathway  693  k1= 0 
  skipping pathway  694  k1= 0 
  skipping pathway  695  k1= 0 
  skipping pathway  696  k1= 0 
  skipping pathway  697  k1= 0 
  skipping pathway  698  k1= 0 
  skipping pathway  699  k1= 0 
  skipping pathway  700  k1= 0 
  skipping pathway  701  k1= 0 
  skipping pathway  702  k1= 0 
  skipping pathway  703  k1= 0 
  skipping pathway  704  k1= 0 
  skipping pathway  705  k1= 0 
  2 pathways processed with start= by ranks 
  ── 1. Error: full pipeline works (@test-all.r#14)  ─────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: lilikoi.select_pathways(PDSmatrix, metaboliteMeasurements, threshold = 0.42, method = "gain") at testthat/test-all.r:14
  2: .lilikoi.plot_significant_pathways(selected_pathways, training_diagnosis)
  3: graphics::plot(q + coord_flip())
  4: plot.ggplot(q + coord_flip())
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
  [1] "1 out of 4 Matched metabolites 60 %"
  [1] "3 out of 4 UnMatched metabolites 40 %"
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "4 out of 5 Matched metabolites 80 %"
  [1] "1 out of 5 UnMatched metabolites 20 %"
  [1] "1 out of 1 Matched metabolites 100 %"
  [1] "0 out of 1 UnMatched metabolites 0 %"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Error: full pipeline works (@test-all.r#14) 
  
  Error: testthat unit tests failed
  Execution halted