Running 'testthat.R' [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
  Sparseness = 99.012 %
  Sorting outcomes by stratumId, time (descending), y and rowId
  Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
  Sparseness = 75.61 %
  Sorting covariates by covariateId and rowId
  Sparseness = 75.695 %
  Sorting covariates by covariateId and rowId
  Sparseness = 75.3 %
  Sorting covariates by covariateId and rowId
  Sparseness = 76.55 %
  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 = -585.503
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #2 Rep #1 pred log like = -596.13
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #3 Rep #1 pred log like = -594.388
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #4 Rep #1 pred log like = -579.469
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #5 Rep #1 pred log like = -609.78
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #6 Rep #1 pred log like = -596.728
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #7 Rep #1 pred log like = -590.234
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #8 Rep #1 pred log like = -569.379
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #9 Rep #1 pred log like = -590.255
  Running at Laplace(4.47214) None  Grid-point #1 at 0.1 	Fold #10 Rep #1 pred log like = -569.965
  AvgPred = -588.183 with stdev = 11.9089
  Completed at 0.1
  Next point at 1 with value 0 and continue = 1
  search[ 0.1 ] = -588.183(11.9089)
  
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #1 Rep #1 pred log like = -587.413
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #2 Rep #1 pred log like = -596.812
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #3 Rep #1 pred log like = -596.513
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #4 Rep #1 pred log like = -580.658
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #5 Rep #1 pred log like = -611.455
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #6 Rep #1 pred log like = -597.123
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #7 Rep #1 pred log like = -591.374
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #8 Rep #1 pred log like = -569.712
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #9 Rep #1 pred log like = -593.857
  Running at Laplace(1.41421) None  Grid-point #2 at 1 	Fold #10 Rep #1 pred log like = -574.289
  AvgPred = -589.921 with stdev = 11.7004
  Completed at 1
  Next point at 0.01 with value 0 and continue = 1
  search[ 0.1 ] = -588.183(11.9089)
  search[ 1 ] = -589.921(11.7004)
  
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #1 Rep #1 pred log like = -583.59
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #2 Rep #1 pred log like = -597.107
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #3 Rep #1 pred log like = -593.164
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #4 Rep #1 pred log like = -577.713
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #5 Rep #1 pred log like = -610.25
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #6 Rep #1 pred log like = -596.412
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #7 Rep #1 pred log like = -591.679
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #8 Rep #1 pred log like = -570.174
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #9 Rep #1 pred log like = -588.619
  Running at Laplace(14.1421) None  Grid-point #3 at 0.01 	Fold #10 Rep #1 pred log like = -568.46
  AvgPred = -587.717 with stdev = 12.3021
  Completed at 0.01
  Next point at 0.001 with value 0 and continue = 1
  search[ 0.01 ] = -587.717(12.3021)
  search[ 0.1 ] = -588.183(11.9089)
  search[ 1 ] = -589.921(11.7004)
  
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #1 Rep #1 pred log like = -594.3
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #2 Rep #1 pred log like = -600.43
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #3 Rep #1 pred log like = -596.386
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #4 Rep #1 pred log like = -585.184
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #5 Rep #1 pred log like = -616.545
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #6 Rep #1 pred log like = -597.987
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #7 Rep #1 pred log like = -594.794
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #8 Rep #1 pred log like = -574.862
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #9 Rep #1 pred log like = -594.09
  Running at Laplace(44.7214) None  Grid-point #4 at 0.001 	Fold #10 Rep #1 pred log like = -578.678
  AvgPred = -593.326 with stdev = 11.1631
  Completed at 0.001
  Next point at 0.0586225 with value -587.372 and continue = 0
  search[ 0.001 ] = -593.326(11.1631)
  search[ 0.01 ] = -587.717(12.3021)
  search[ 0.1 ] = -588.183(11.9089)
  search[ 1 ] = -589.921(11.7004)
  
  
  Maximum predicted log likelihood (-587.372) estimated at:
  	0.0586225 (variance)
  	5.84094 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(5.84094) None 
  Using cross-validation selector type byRow
  Performing 10-fold cross-validation [seed = 1585935694] 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 = -14.1379
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #2 Rep #1 pred log like = -2.77055
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #3 Rep #1 pred log like = -9.40993
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #4 Rep #1 pred log like = -5.31322
  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 = -15.8475
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #7 Rep #1 pred log like = -7.51911
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #8 Rep #1 pred log like = -2.95363
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #9 Rep #1 pred log like = -4.84215
  Running at Laplace(2.44949) None  Grid-point #1 at 0.333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -6.50034 with stdev = 4.96509
  Completed at 0.333333
  Next point at 3.33333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50034(4.96509)
  
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #1 Rep #1 pred log like = -16.7876
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #2 Rep #1 pred log like = -3.50648
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #3 Rep #1 pred log like = -9.85821
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #4 Rep #1 pred log like = -5.39944
  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 = -15.784
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #7 Rep #1 pred log like = -9.67073
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #8 Rep #1 pred log like = -3.10646
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #9 Rep #1 pred log like = -4.87441
  Running at Laplace(0.774597) None  Grid-point #2 at 3.33333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -7.11952 with stdev = 5.42701
  Completed at 3.33333
  Next point at 0.0333333 with value 0 and continue = 1
  search[ 0.333333 ] = -6.50034(4.96509)
  search[ 3.33333 ] = -7.11952(5.42701)
  
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #1 Rep #1 pred log like = -8.56419
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #2 Rep #1 pred log like = -2.38933
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #3 Rep #1 pred log like = -8.20109
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #4 Rep #1 pred log like = -4.23476
  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 = -17.2486
  Running at Laplace(7.74597) None  Grid-point #3 at 0.0333333 	Fold #7 Rep #1 pred log like = -6.4016
  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 = -5.03781
  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 ] = -6.50034(4.96509)
  search[ 3.33333 ] = -7.11952(5.42701)
  
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #1 Rep #1 pred log like = -8.76107
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #2 Rep #1 pred log like = -2.40094
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #3 Rep #1 pred log like = -10.0062
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #4 Rep #1 pred log like = -3.17613
  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 = -17.9197
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #7 Rep #1 pred log like = -4.82178
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #8 Rep #1 pred log like = -2.43581
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #9 Rep #1 pred log like = -5.61866
  Running at Laplace(24.4949) None  Grid-point #4 at 0.00333333 	Fold #10 Rep #1 pred log like = 0
  AvgPred = -5.7731 with stdev = 4.9802
  Completed at 0.00333333
  Next point at 0.00420369 with value -5.71924 and continue = 0
  search[ 0.00333333 ] = -5.7731(4.9802)
  search[ 0.0333333 ] = -5.71402(4.63275)
  search[ 0.333333 ] = -6.50034(4.96509)
  search[ 3.33333 ] = -7.11952(5.42701)
  
  
  Maximum predicted log likelihood (-5.71924) estimated at:
  	0.00420369 (variance)
  	21.8122 (lambda)
  
  Fitting model at optimal hyperparameter
  Using prior: Laplace(21.8122) None 
  -- 1. Failure: Test basic XY constructor (@test-xyConstructor.R#29)  -----------
  summary(dataPtrD)[, "type"] not equal to as.factor(rep("dense", 5)).
  Types not compatible: character is not integer
  
  -- 2. Failure: Test basic XY constructor (@test-xyConstructor.R#40)  -----------
  summary(dataPtrI)[, "type"] not equal to as.factor(rep("indicator", 5)).
  Types not compatible: character is not integer
  
  -- 3. Failure: Test basic XY constructor (@test-xyConstructor.R#51)  -----------
  summary(dataPtrS)[, "type"] not equal to as.factor(rep("sparse", 5)).
  Types not compatible: character is not integer
  
  -- 4. Failure: Test COO-constructor (@test-xyConstructor.R#182)  ---------------
  summary(dataPtrI)[, "type"] not equal to as.factor(rep("indicator", 5)).
  Types not compatible: character is not integer
  
  -- 5. Failure: Test COO-constructor (@test-xyConstructor.R#191)  ---------------
  summary(dataPtrS)[, "type"] not equal to as.factor(rep("sparse", 5)).
  Types not compatible: character is not integer
  
  -- 6. Failure: Test COO-constructor (@test-xyConstructor.R#207)  ---------------
  summary(dataPtrA)[, "type"] not equal to as.factor(rep("indicator", 5)).
  Types not compatible: character is not integer
  
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  == testthat results  ===========================================================
  [ OK: 245 | SKIPPED: 11 | WARNINGS: 195 | FAILED: 6 ]
  1. Failure: Test basic XY constructor (@test-xyConstructor.R#29) 
  2. Failure: Test basic XY constructor (@test-xyConstructor.R#40) 
  3. Failure: Test basic XY constructor (@test-xyConstructor.R#51) 
  4. Failure: Test COO-constructor (@test-xyConstructor.R#182) 
  5. Failure: Test COO-constructor (@test-xyConstructor.R#191) 
  6. Failure: Test COO-constructor (@test-xyConstructor.R#207) 
  
  Error: testthat unit tests failed
  Execution halted