Running ‘testthat.R’ [18s/20s]
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 = -503.995
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #2 Rep #1 pred log like = -514.462
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #3 Rep #1 pred log like = -454.185
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #4 Rep #1 pred log like = -503.103
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #5 Rep #1 pred log like = -479.465
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #6 Rep #1 pred log like = -501.782
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #7 Rep #1 pred log like = -498.809
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #8 Rep #1 pred log like = -489.977
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #9 Rep #1 pred log like = -520.765
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #10 Rep #1 pred log like = -475.471
  AvgPred = -494.201 with stdev = 18.8603
  Completed at 0.1
  Next point at 1 with value 0 and continue = 1
  search[ 0.1 ] = -494.201(18.8603)
  
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #1 Rep #1 pred log like = -505.713
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #2 Rep #1 pred log like = -517.702
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #3 Rep #1 pred log like = -457.65
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #4 Rep #1 pred log like = -506.287
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #5 Rep #1 pred log like = -482.998
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #6 Rep #1 pred log like = -502.747
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #7 Rep #1 pred log like = -502.508
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #8 Rep #1 pred log like = -491.835
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #9 Rep #1 pred log like = -524.234
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #10 Rep #1 pred log like = -475.74
  AvgPred = -496.741 with stdev = 19.0216
  Completed at 1
  Next point at 0.01 with value 0 and continue = 1
  search[ 0.1 ] = -494.201(18.8603)
  search[ 1 ] = -496.741(19.0216)
  
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #1 Rep #1 pred log like = -503.087
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #2 Rep #1 pred log like = -511.157
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #3 Rep #1 pred log like = -452.452
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #4 Rep #1 pred log like = -502.937
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #5 Rep #1 pred log like = -478.714
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #6 Rep #1 pred log like = -502.323
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #7 Rep #1 pred log like = -499.72
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #8 Rep #1 pred log like = -491.143
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #9 Rep #1 pred log like = -519.968
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #10 Rep #1 pred log like = -477.689
  AvgPred = -493.919 with stdev = 18.6202
  Completed at 0.01
  Next point at 0.001 with value 0 and continue = 1
  search[ 0.01 ] = -493.919(18.6202)
  search[ 0.1 ] = -494.201(18.8603)
  search[ 1 ] = -496.741(19.0216)
  
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #1 Rep #1 pred log like = -504.638
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #2 Rep #1 pred log like = -514.529
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #3 Rep #1 pred log like = -454.911
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #4 Rep #1 pred log like = -507.457
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #5 Rep #1 pred log like = -483.687
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #6 Rep #1 pred log like = -504.638
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #7 Rep #1 pred log like = -506.046
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #8 Rep #1 pred log like = -494.82
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #9 Rep #1 pred log like = -520.214
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #10 Rep #1 pred log like = -483.687
  AvgPred = -497.463 with stdev = 18.1178
  Completed at 0.001
  Next point at 0.0364682 with value -493.672 and continue = 0
  search[ 0.001 ] = -497.463(18.1178)
  search[ 0.01 ] = -493.919(18.6202)
  search[ 0.1 ] = -494.201(18.8603)
  search[ 1 ] = -496.741(19.0216)
  
  
  Maximum predicted log likelihood (-493.672) estimated at:
  	0.0364682 (variance)
  	7.40556 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(7.40556) 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 == -0.448
  
  Using cross-validation selector type byRow
  Performing 10-fold cross-validation [seed = 1552132072] 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 = -9.40993
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #3 Rep #1 pred log like = -15.8481
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #4 Rep #1 pred log like = -2.77049
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #5 Rep #1 pred log like = -2.20943
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #6 Rep #1 pred log like = -14.1377
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #7 Rep #1 pred log like = -4.84229
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #8 Rep #1 pred log like = -7.51909
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #9 Rep #1 pred log like = -2.95363
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -6.50039 with stdev = 4.96517
  Completed at 0.333333
  Next point at 3.33333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50039(4.96517)
  
  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 = -9.85805
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #3 Rep #1 pred log like = -15.784
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #4 Rep #1 pred log like = -3.50406
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #5 Rep #1 pred log like = -2.20787
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #6 Rep #1 pred log like = -16.7877
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #7 Rep #1 pred log like = -4.90174
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #8 Rep #1 pred log like = -9.6661
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #9 Rep #1 pred log like = -3.10646
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -7.12154 with stdev = 5.42582
  Completed at 3.33333
  Next point at 0.0333333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50039(4.96517)
  search[ 3.33333 ] = -7.12154(5.42582)
  
  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 = -8.20108
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #3 Rep #1 pred log like = -17.2486
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #4 Rep #1 pred log like = -2.38932
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #5 Rep #1 pred log like = -2.22488
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #6 Rep #1 pred log like = -8.56406
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #7 Rep #1 pred log like = -5.03779
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #8 Rep #1 pred log like = -6.4016
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #9 Rep #1 pred log like = -2.8379
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -5.714 with stdev = 4.63274
  Completed at 0.0333333
  Next point at 0.00333333 with value 0 and continue = 1
  search[ 0.0333333 ] = -5.714(4.63274)
  search[ 0.333333 ] = -6.50039(4.96517)
  search[ 3.33333 ] = -7.12154(5.42582)
  
  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 = -10.0062
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #3 Rep #1 pred log like = -17.9197
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #4 Rep #1 pred log like = -2.40094
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #5 Rep #1 pred log like = -2.59079
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #6 Rep #1 pred log like = -8.76107
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #7 Rep #1 pred log like = -5.61869
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #8 Rep #1 pred log like = -4.82178
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #9 Rep #1 pred log like = -2.43581
  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 0.00422501 with value -5.71926 and continue = 0
  search[ 0.00333333 ] = -5.77311(4.9802)
  search[ 0.0333333 ] = -5.714(4.63274)
  search[ 0.333333 ] = -6.50039(4.96517)
  search[ 3.33333 ] = -7.12154(5.42582)
  
  
  Maximum predicted log likelihood (-5.71926) estimated at:
  	0.00422501 (variance)
  	21.7571 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(21.7571) 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