Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("Cyclops")
  Loading required package: Cyclops
  Sorting outcomes by stratumId and rowId
  Sorting covariates by covariateId, stratumId, and rowId
  Sorting outcomes by stratumId and rowId
  Sorting covariates by covariateId, stratumId and rowId
  Sorting outcomes by stratumId and rowId
  Sorting covariates by covariateId, stratumId, and rowId
  Sorting outcomes by stratumId, time (descending), y, and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId, time (descending), y, and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sparseness = 76.245 %
  Sorting covariates by covariateId, stratumId and rowId
  Sorting covariates by covariateId, stratumId, and rowId
  Sorting outcomes by stratumId, time (descending), y, and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sparseness = 75.76 %
  Sorting covariates by covariateId, rowId
  Sorting covariates by covariateId and rowId
  Sparseness = 99.012 %
  Sorting covariates by covariateId and rowId
  -- 1. Failure: Separable covariates in logistic regression (@test-largeBernoulli
  `coef(fit)` did not throw an error.
  
  -- 2. Failure: Separable covariates in logistic regression (@test-largeBernoulli
  coef(ecFit)[separability] not equivalent to 0.
  Lengths differ: 0 is not 1
  
  -- 3. Failure: Separable covariates in logistic regression (@test-largeBernoulli
  is.na(coef(nsFit)[7]) isn't true.
  
  Sparseness = 99.012 %
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sparseness = 76.145 %
  Sorting covariates by covariateId and rowId
  Sparseness = 75.035 %
  Sorting covariates by covariateId and rowId
  Sparseness = 75.5 %
  Sorting covariates by covariateId and rowId
  Sparseness = 76.95 %
  Sorting covariates by covariateId and rowId
  Sparseness = 99.012 %
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sparseness = 98.0118 %
  Sorting covariates by covariateId and rowId
  Using cross-validation selector type byRow
  Performing 10-fold cross-validation [seed = 123] with data partitions of sizes 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
  Using 1 thread(s)
  Starting var = 0.1
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #1 Rep #1 pred log like = -489.699
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #2 Rep #1 pred log like = -493.537
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #3 Rep #1 pred log like = -502.437
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #4 Rep #1 pred log like = -476.269
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #5 Rep #1 pred log like = -505.784
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #6 Rep #1 pred log like = -485.599
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #7 Rep #1 pred log like = -489.158
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #8 Rep #1 pred log like = -482.34
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #9 Rep #1 pred log like = -514.145
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #10 Rep #1 pred log like = -503.564
  AvgPred = -494.253 with stdev = 11.2685
  Completed at 0.1
  Next point at 1 with value 0 and continue = 1
  search[ 0.1 ] = -494.253(11.2685)
  
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #1 Rep #1 pred log like = -494.698
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #2 Rep #1 pred log like = -495.573
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #3 Rep #1 pred log like = -502.68
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #4 Rep #1 pred log like = -478.07
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #5 Rep #1 pred log like = -506.81
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #6 Rep #1 pred log like = -487.935
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #7 Rep #1 pred log like = -491.118
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #8 Rep #1 pred log like = -486.513
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #9 Rep #1 pred log like = -521.055
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #10 Rep #1 pred log like = -505.658
  AvgPred = -497.011 with stdev = 11.724
  Completed at 1
  Next point at 0.01 with value 0 and continue = 1
  search[ 0.1 ] = -494.253(11.2685)
  search[ 1 ] = -497.011(11.724)
  
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #1 Rep #1 pred log like = -486.897
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #2 Rep #1 pred log like = -494.035
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #3 Rep #1 pred log like = -502.626
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #4 Rep #1 pred log like = -476.177
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #5 Rep #1 pred log like = -506.808
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #6 Rep #1 pred log like = -485.72
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #7 Rep #1 pred log like = -490.237
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #8 Rep #1 pred log like = -480.72
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #9 Rep #1 pred log like = -511.622
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #10 Rep #1 pred log like = -504.56
  AvgPred = -493.94 with stdev = 11.3473
  Completed at 0.01
  Next point at 0.001 with value 0 and continue = 1
  search[ 0.01 ] = -493.94(11.3473)
  search[ 0.1 ] = -494.253(11.2685)
  search[ 1 ] = -497.011(11.724)
  
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #1 Rep #1 pred log like = -492.028
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #2 Rep #1 pred log like = -499.019
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #3 Rep #1 pred log like = -501.832
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #4 Rep #1 pred log like = -476.777
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #5 Rep #1 pred log like = -511.696
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #6 Rep #1 pred log like = -489.242
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #7 Rep #1 pred log like = -496.218
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #8 Rep #1 pred log like = -482.302
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #9 Rep #1 pred log like = -515.948
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #10 Rep #1 pred log like = -508.868
  AvgPred = -497.393 with stdev = 12.0508
  Completed at 0.001
  Next point at 0.0335887 with value -493.708 and continue = 0
  search[ 0.001 ] = -497.393(12.0508)
  search[ 0.01 ] = -493.94(11.3473)
  search[ 0.1 ] = -494.253(11.2685)
  search[ 1 ] = -497.011(11.724)
  
  
  Maximum predicted log likelihood (-493.708) estimated at:
  	0.0335887 (variance)
  	7.71647 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(7.71647) None 
  -- 4. Failure: Logistic regression with cross-validation (@test-weighted_cv.R#26
  coef(fit)[1] not equal to -0.99.
  1/1 mismatches
  [1] -1.44 - -0.99 == -0.447
  
  Using cross-validation selector type byRow
  Performing 10-fold cross-validation [seed = 1551697371] with data partitions of sizes 1 1 1 1 1 1 1 1 1 0
  Using 1 thread(s)
  Starting var = 0.333333 (default)
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #1 Rep #1 pred log like = -5.31322
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #2 Rep #1 pred log like = -15.8482
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #3 Rep #1 pred log like = -2.77049
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #4 Rep #1 pred log like = -9.40993
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #5 Rep #1 pred log like = -4.84215
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #6 Rep #1 pred log like = -7.51905
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #7 Rep #1 pred log like = -14.1377
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #8 Rep #1 pred log like = -2.95357
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #9 Rep #1 pred log like = -2.20943
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -6.50037 with stdev = 4.9652
  Completed at 0.333333
  Next point at 3.33333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50037(4.9652)
  
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #1 Rep #1 pred log like = -5.39944
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #2 Rep #1 pred log like = -15.7841
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #3 Rep #1 pred log like = -3.50406
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #4 Rep #1 pred log like = -7.79048
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #5 Rep #1 pred log like = -4.90174
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #6 Rep #1 pred log like = -9.6661
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #7 Rep #1 pred log like = -16.7877
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #8 Rep #1 pred log like = -3.10734
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #9 Rep #1 pred log like = -2.20787
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -6.91488 with stdev = 5.35651
  Completed at 3.33333
  Next point at 0.0333333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50037(4.9652)
  search[ 3.33333 ] = -6.91488(5.35651)
  
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #1 Rep #1 pred log like = -4.23478
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #2 Rep #1 pred log like = -17.2486
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #3 Rep #1 pred log like = -2.38932
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #4 Rep #1 pred log like = -8.20109
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #5 Rep #1 pred log like = -5.03777
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #6 Rep #1 pred log like = -6.4016
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #7 Rep #1 pred log like = -8.56421
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #8 Rep #1 pred log like = -2.8379
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #9 Rep #1 pred log like = -2.22488
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -5.71402 with stdev = 4.63275
  Completed at 0.0333333
  Next point at 0.00333333 with value 0 and continue = 1
  search[ 0.0333333 ] = -5.71402(4.63275)
  search[ 0.333333 ] = -6.50037(4.9652)
  search[ 3.33333 ] = -6.91488(5.35651)
  
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #1 Rep #1 pred log like = -3.17616
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #2 Rep #1 pred log like = -17.9197
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #3 Rep #1 pred log like = -2.40094
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #4 Rep #1 pred log like = -10.0062
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #5 Rep #1 pred log like = -5.61869
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #6 Rep #1 pred log like = -4.82178
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #7 Rep #1 pred log like = -8.76107
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #8 Rep #1 pred log like = -2.4358
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #9 Rep #1 pred log like = -2.59079
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -5.77311 with stdev = 4.9802
  Completed at 0.00333333
  Next point at 0.00197495 with value -5.70408 and continue = 0
  search[ 0.00333333 ] = -5.77311(4.9802)
  search[ 0.0333333 ] = -5.71402(4.63275)
  search[ 0.333333 ] = -6.50037(4.9652)
  search[ 3.33333 ] = -6.91488(5.35651)
  
  
  Maximum predicted log likelihood (-5.70408) estimated at:
  	0.00197495 (variance)
  	31.8227 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(31.8227) None 
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  == testthat results  ===========================================================
  OK: 249 SKIPPED: 11 FAILED: 4
  1. Failure: Separable covariates in logistic regression (@test-largeBernoulli.R#43) 
  2. Failure: Separable covariates in logistic regression (@test-largeBernoulli.R#62) 
  3. Failure: Separable covariates in logistic regression (@test-largeBernoulli.R#67) 
  4. Failure: Logistic regression with cross-validation (@test-weighted_cv.R#26) 
  
  Error: testthat unit tests failed
  Execution halted