Running ‘testthat.R’ [4m/30m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("CohortMethod")
  Loading required package: CohortMethod
  Loading required package: DatabaseConnector
  Loading required package: Cyclops
  Loading required package: FeatureExtraction
  Loading required package: Andromeda
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  attempting to download GiBleed
  trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
  Content type 'application/zip' length 6861852 bytes (6.5 MB)
  ==================================================
  downloaded 6.5 MB
  
  attempting to extract and load: /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/GiBleed_5.3.zip to: /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/GiBleed_5.3.sqlite
  Cohorts created in table main.cohort
  Saving _problems/test-balance-14.R
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1797, total rows in comparator is 830
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 2.54 secs
  Fetched covariates total count is 26893
  Fetched outcomes total count is 3106
  Calling getDbCohortMethodData() for targetId 1, comparatorId 999
  Fetched cohort total rows in target is 1800, total rows in comparator is 0
  Constructing features on server
  Fetching data from server
  Fetching data took 2.55 secs
  Fetched covariates total count is 24166
  Fetched outcomes total count is 2155
  Calling getDbCohortMethodData() for targetId 998, comparatorId 999
  Fetched cohort total rows in target is 0, total rows in comparator is 0
  Fetched covariates total count is 0
  Fetched outcomes total count is 0
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2627 rows
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t1_c999.zip for outcomeId 3
  Study population has 1800 rows
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t998_c999.zip for outcomeId 3
  Study population has 0 rows
  Initiating cluster consisting only of main thread
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t1_c2.zip
  Study population has 2627 rows
  Removing 6 redundant covariates
  Removing 112 infrequent covariates
  Normalizing covariates
  Tidying covariates took 17.2 secs
  Propensity model fitting finished with status OK
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t1_c999.zip
  Study population has 1800 rows
  Propensity model fitting finished with status Target or comparator cohort empty, so cannot fit model
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t998_c999.zip
  Study population has 0 rows
  Propensity model fitting finished with status No subjects in population, so cannot fit model
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c2_o3.rds
  Population size after matching is 1660
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c999_o3.rds
  Population size after matching is 0
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t998_c999_o3.rds
  Population size after matching is 0
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c2_o3.rds
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c999_o3.rds
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c2_o3.rds
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c999_o3.rds
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c2_o3.rds
  Removed 0 (0.0%) rows from the target, 0 (0.0%) rows from the comparator not in overlap.
  Trimming removed 0 (0.0%) rows from the target, 3 (0.4%) rows from the comparator in total.
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t1_c999_o3.rds
  Removed 0 (0.0%) rows from the target, 0 (NaN%) rows from the comparator not in overlap.
  Trimming removed 0 (0.0%) rows from the target, 0 (NaN%) rows from the comparator in total.
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/Ps_l1_s1_p2_t998_c999_o3.rds
  Removed 0 (NaN%) rows from the target, 0 (NaN%) rows from the comparator not in overlap.
  Trimming removed 0 (NaN%) rows from the target, 0 (NaN%) rows from the comparator in total.
  Initiating cluster consisting only of main thread
  Computing shared balance using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a41129545/CmData_l1_t1_c2.zip
  Study population has 2627 rows
  Population size after matching is 1660
  Saving _problems/test-eunomia-246.R
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1797, total rows in comparator is 830
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 3.36 secs
  Fetched covariates total count is 5254
  Fetched outcomes total count is 3106
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2627 rows
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip for outcomeId 4
  Study population has 2627 rows
  Initiating cluster consisting only of main thread
  Calling createPs() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/StudyPop_l1_s1_t1_c2_o3.rds
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 15.7 secs
  Propensity model fitting finished with status OK
  Calling createPs() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/StudyPop_l1_s1_t1_c2_o4.rds
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 13.2 secs
  Propensity model fitting finished with status OK
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/Ps_l1_s1_p1_t1_c2_o3.rds
  Population size after matching is 1660
  Initiating cluster consisting only of main thread
  Calling fitOutcomeModel() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/StratPop_l1_s1_p1_t1_c2_s1_o3.rds
  Using prior: None 
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Outcome model fitting status is: OK
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation(), performing matching etc., and calling fitOutcomeModel() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a47dff62b/CmData_l1_t1_c2.zip for outcomeID 4
  Study population has 2627 rows
  Population size after matching is 1660
  Using prior: None 
  
  Warning: BLR gradient is ill-conditioned
  Enforcing convergence!
  Using prior: None 
  
  Warning: BLR gradient is ill-conditioned
  Enforcing convergence!
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Outcome model fitting status is: POOR_BLR_STEP
  
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  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1800, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 2.48 secs
  Fetched covariates total count is 2730
  Fetched outcomes total count is 479
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a2b1a57c1/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2630 rows
  Initiating cluster consisting only of main thread
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a2b1a57c1/CmData_l1_t1_c2.zip
  Study population has 2630 rows
  Removing 0 redundant covariates
  Removing 10 infrequent covariates
  Normalizing covariates
  Tidying covariates took 11.2 secs
  Propensity model fitting finished with status High correlation between covariate(s) and treatment detected. Perhaps you forgot to exclude part of the exposure definition from the covariates?
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a2b1a57c1/Ps_l1_s1_p1_t1_c2_o3.rds
  Population size after matching is 0
  Initiating cluster consisting only of main thread
  Calling fitOutcomeModel() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a2b1a57c1/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a2b1a57c1/StratPop_l1_s1_p1_t1_c2_s1_o3.rds
  Outcome model fitting status is: NO SUBJECTS IN POPULATION, CANNOT FIT
  
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  Initiating cluster consisting only of main thread
  
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  Initiating cluster consisting only of main thread
  Preparing KM plot for target_comparator 894409308, outcome 3, analysis 1
  
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    |======================================================================| 100%
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1800, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 3.56 secs
  Fetched covariates total count is 5260
  Fetched outcomes total count is 479
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2630 rows
  Initiating cluster consisting only of main thread
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/CmData_l1_t1_c2.zip
  Study population has 2630 rows
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 37 secs
  Propensity model fitting finished with status OK
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/Ps_l1_s1_p1_t1_c2_o3.rds
  Population size after matching is 1660
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/Ps_l1_s1_p1_t1_c2_o3.rds
  Initiating cluster consisting only of main thread
  Calling fitOutcomeModel() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/StratPop_l1_s1_p1_t1_c2_s1_o3.rds
  Using prior: None 
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Outcome model fitting status is: OK
  Calling fitOutcomeModel() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/CmData_l1_t1_c2.zip and /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6efa4c83/StratPop_l1_s1_p1_t1_c2_s2_o3.rds
  Using prior: None 
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Using 1 thread(s)
  Outcome model fitting status is: OK
  
    |                                                                            
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    |======================================================================| 100%
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1800, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 20 secs
  Fetched covariates total count is 5260
  Fetched outcomes total count is 479
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1800, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 4.35 secs
  Fetched covariates total count is 5260
  Fetched outcomes total count is 479
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/CmData_l1_t1_c2_n4.zip for outcomeId 3
  Study population has 2630 rows
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2630 rows
  Initiating cluster consisting only of main thread
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/CmData_l1_t1_c2_n4.zip
  Study population has 2630 rows
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 2.84 secs
  Propensity model fitting finished with status OK
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/CmData_l1_t1_c2.zip
  Study population has 2630 rows
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 7.41 secs
  Propensity model fitting finished with status OK
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/Ps_l1_s1_p1_t1_c2_n4_o3.rds
  Population size after matching is 1660
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/Ps_l1_s1_p1_t1_c2_o3.rds
  Population size after matching is 1660
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/Ps_l1_s1_p1_t1_c2_n4_o3.rds
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/Ps_l1_s1_p1_t1_c2_o3.rds
  Initiating cluster consisting only of main thread
  Computing shared balance using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a6b904e92/CmData_l1_t1_c2_n4.zip
  Study population has 2630 rows
  Population size after matching is 1660
  Saving _problems/test-eunomia-692.R
  Initiating cluster consisting only of main thread
  Calling getDbCohortMethodData() for targetId 1, comparatorId 2
  Fetched cohort total rows in target is 1800, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 0.862 secs
  Fetched covariates total count is 5260
  Fetched outcomes total count is 479
  Initiating cluster consisting only of main thread
  Calling createStudyPopulation() using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a13ce3bbd/CmData_l1_t1_c2.zip for outcomeId 3
  Study population has 2630 rows
  Initiating cluster consisting only of main thread
  Calling createPs() for shared PS using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a13ce3bbd/CmData_l1_t1_c2.zip
  Study population has 2630 rows
  Removing 1 redundant covariates
  Removing 0 infrequent covariates
  Normalizing covariates
  Tidying covariates took 6.91 secs
  Propensity model fitting finished with status OK
  Initiating cluster consisting only of main thread
  Initiating cluster consisting only of main thread
  Performing matching etc., using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a13ce3bbd/Ps_l1_s1_p1_t1_c2_o3.rds
  Population size after matching is 1660
  Initiating cluster consisting only of main thread
  Computing shared balance using /tmp/RtmpLS9hAh/working_dir/RtmpzcY86S/cmData1ae95a13ce3bbd/CmData_l1_t1_c2.zip
  Study population has 2630 rows
  Population size after matching is 1660
  Saving _problems/test-eunomia-827.R
  Fetched cohort total rows in target is 1797, total rows in comparator is 830
  Sending temp tables to server
  Constructing features on server
  Fetching data from server
  Fetching data took 4.65 secs
  Fetched covariates total count is 26893
  Fetched outcomes total count is 3106
  Fetched cohort total rows in target is 885, total rows in comparator is 386
  Constructing features on server
  Fetching data from server
  Fetching data took 1.11 secs
  Fetched covariates total count is 1271
  Fetched outcomes total count is 1510
  Fetched cohort total rows in target is 1797, total rows in comparator is 830
  Constructing features on server
  Fetching data from server
  Fetching data took 9.8 secs
  Fetched covariates total count is 2627
  Fetched outcomes total count is 3106
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 1.14 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 941, total rows in comparator is 941
  Constructing features on server
  Fetching data from server
  Fetching data took 0.675 secs
  Fetched covariates total count is 1882
  Fetched outcomes total count is 2179
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 2.19 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 478, total rows in comparator is 522
  Constructing features on server
  Fetching data from server
  Fetching data took 2.57 secs
  Fetched covariates total count is 1000
  Fetched outcomes total count is 1158
  Fetched cohort total rows in target is 478, total rows in comparator is 522
  Constructing features on server
  Fetching data from server
  Fetching data took 1.12 secs
  Fetched covariates total count is 1000
  Fetched outcomes total count is 1158
  Fetched cohort total rows in target is 236, total rows in comparator is 236
  Constructing features on server
  Fetching data from server
  Fetching data took 1.19 secs
  Fetched covariates total count is 472
  Fetched outcomes total count is 548
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 2.15 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 1998, total rows in comparator is 2000
  Constructing features on server
  Fetching data from server
  Fetching data took 1.81 secs
  Fetched covariates total count is 3998
  Fetched outcomes total count is 4629
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 1.16 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 1203, total rows in comparator is 1223
  Constructing features on server
  Fetching data from server
  Fetching data took 1.01 secs
  Fetched covariates total count is 2426
  Fetched outcomes total count is 2796
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 0.601 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 988, total rows in comparator is 984
  Constructing features on server
  Fetching data from server
  Fetching data took 0.663 secs
  Fetched covariates total count is 1972
  Fetched outcomes total count is 2284
  Fetched cohort total rows in target is 1998, total rows in comparator is 2002
  Constructing features on server
  Fetching data from server
  Fetching data took 0.566 secs
  Fetched covariates total count is 4000
  Fetched outcomes total count is 4632
  Fetched cohort total rows in target is 797, total rows in comparator is 783
  Constructing features on server
  Fetching data from server