Running ‘testthat.R’ [35s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MBMethPred)
  > 
  > test_check("MBMethPred")
          y_pred
  y_true   Group3 SHH Group4
    Group3      1   0      0
    SHH         1   1      0
    Group4      0   0      1
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3      8   0   0      0
    SHH         0  24   2      0
    WNT         0   0  24      0
    Group4      1   0   0     31
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     20   0   0      1
    SHH         0  20   0      0
    WNT         0   0  18      0
    Group4      1   0   0     32
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     18   0   0      1
    SHH         0  41   0      0
    WNT         0   0  37      0
    Group4      6   2   0     52
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     26   0   1      0
    SHH         0  41   0      0
    WNT         0   0  38      0
    Group4      1   1   0     53
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     27   0   0      0
    SHH         0  43   0      0
    WNT         0   0  37      0
    Group4      4   2   0     54
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     23   0   0      3
    SHH         0  42   0      0
    WNT         0   0  35      0
    Group4      6   1   0     55
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     26   0   0      1
    SHH         0  38   1      0
    WNT         0   0  39      0
    Group4      5   0   0     52
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     26   0   0      2
    SHH         0  41   0      0
    WNT         0   0  39      0
    Group4      0   0   0     57
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     27   0   0      2
    SHH         0  41   0      0
    WNT         0   0  39      0
    Group4      3   1   1     53
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     21   0   0      3
    SHH         0  42   0      0
    WNT         0   0  37      0
    Group4      6   0   0     54
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     20   0   1      5
    SHH         0  42   0      0
    WNT         0   0  37      0
    Group4      6   1   0     46
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     27   0   0      1
    SHH         0  41   1      0
    WNT         0   0  40      0
    Group4      6   0   0     57
  
  Saving _problems/test-ModelMetrics-2.R
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     13   0   0      0
    SHH         0  27   0      0
    WNT         0   0  22      1
    Group4      1   0   0     24
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     15   0   0      1
    SHH         0  19   0      0
    WNT         0   0  19      0
    Group4      4   0   0     36
  
  Saving _problems/test-NewDataPredictionResult-10.R
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     15   0   0      2
    SHH         0  18   0      0
    WNT         0   0  18      0
    Group4      0   0   0     34
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     11   0   0      1
    SHH         0  27   0      1
    WNT         0   0  24      0
    Group4      0   0   0     31
  
  The NMI score is: 0.903790812437385
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     12   0   0      1
    SHH         0  26   0      0
    WNT         1   0  20      0
    Group4      0   0   0     31
  
          y_pred
  y_true   Group3 SHH WNT Group4
    Group3     15   0   0      1
    SHH         0  20   0      0
    WNT         0   0  21      0
    Group4      2   0   0     32
  
  Saving _problems/test-XGBoostModel-2.R
  [ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ModelMetrics.r:2:3'): ModelMetrics returns correct class. ──────
  Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
  Backtrace:
      ▆
   1. └─MBMethPred::XGBoostModel(...) at test-ModelMetrics.r:2:3
   2.   └─parallel::mclapply(...)
   3.     └─base::lapply(X = X, FUN = FUN, ...)
   4.       └─MBMethPred (local) FUN(X[[i]], ...)
   5.         └─xgboost::xgboost(...)
   6.           └─xgboost:::prescreen.objective(objective)
  ── Error ('test-NewDataPredictionResult.R:10:3'): NewDataPredictionResult returns correct type ──
  Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
  Backtrace:
      ▆
   1. └─MBMethPred::XGBoostModel(...) at test-NewDataPredictionResult.R:10:3
   2.   └─parallel::mclapply(...)
   3.     └─base::lapply(X = X, FUN = FUN, ...)
   4.       └─MBMethPred (local) FUN(X[[i]], ...)
   5.         └─xgboost::xgboost(...)
   6.           └─xgboost:::prescreen.objective(objective)
  ── Error ('test-XGBoostModel.R:2:3'): XGBoostModel returns correct class. ──────
  Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
  Backtrace:
      ▆
   1. ├─testthat::expect_type(...) at test-XGBoostModel.R:2:3
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─MBMethPred::XGBoostModel(...)
   5.   └─parallel::mclapply(...)
   6.     └─base::lapply(X = X, FUN = FUN, ...)
   7.       └─MBMethPred (local) FUN(X[[i]], ...)
   8.         └─xgboost::xgboost(...)
   9.           └─xgboost:::prescreen.objective(objective)
  
  [ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
  Error:
  ! Test failures.
  Execution halted