Running ‘testthat.R’ [10m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(PhenotypeR)
  > 
  > test_check("PhenotypeR")
  Creating a new cdm
  Uploading table person (100 rows) - [1/13]
  Uploading table observation_period (100 rows) - [2/13]
  Uploading table cdm_source (1 rows) - [3/13]
  Uploading table concept (3361 rows) - [4/13]
  Uploading table vocabulary (65 rows) - [5/13]
  Uploading table concept_relationship (117257 rows) - [6/13]
  Uploading table concept_synonym (3895 rows) - [7/13]
  Uploading table concept_ancestor (1327 rows) - [8/13]
  Uploading table drug_strength (45 rows) - [9/13]
  Uploading table condition_occurrence (600 rows) - [10/13]
  Uploading table drug_exposure (3100 rows) - [11/13]
  Uploading table measurement (2000 rows) - [12/13]
  Uploading table my_cohort_1 (100 rows) - [13/13]
  i Subsetting table measurement using 20 concepts with domain: measurement.
  i Combining tables.
  i Creating cohort attributes.
  i Applying cohort requirements.
  i Merging overlapping records.
  v Cohort measurement_cohort created.
  Getting counts of all_measurements codes for cohort all_measurements
  > Getting measurement records based on 20 concepts.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:41:26.030413
  v Summary finished, at 2026-02-23 19:41:26.292266
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:41:27.783403
  v Summary finished, at 2026-02-23 19:41:28.008126
  i summarising data
  i summarising cohort all_measurements
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:41:35.215436
  v Summary finished, at 2026-02-23 19:41:36.461469
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:41:38.589383
  v Summary finished, at 2026-02-23 19:41:38.976004
  > Binding all diagnostic results.
  Getting counts of all_measurements codes for cohort all_measurements
  > Getting measurement records based on 20 concepts.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:41:59.522023
  v Summary finished, at 2026-02-23 19:41:59.932363
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:42:01.439235
  v Summary finished, at 2026-02-23 19:42:01.679716
  i summarising data
  i summarising cohort all_measurements
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:42:09.45296
  v Summary finished, at 2026-02-23 19:42:11.046864
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:42:13.111596
  v Summary finished, at 2026-02-23 19:42:13.613935
  > Binding all diagnostic results.
  Saving _problems/test-codelistDiagnostics-129.R
  Getting counts of all_measurements codes for cohort all_measurements
  i Subsetting table measurement using 20 concepts with domain: measurement.
  i Combining tables.
  i Creating cohort attributes.
  i Applying cohort requirements.
  i Merging overlapping records.
  v Cohort measurement_2 created.
  Getting counts of all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
  Getting counts of all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
  Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
  Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
  Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
  Getting counts of all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
  Getting counts of all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
  Getting counts of all_measurements_alkaline_phosphatase_isoenzymes_measurement codes for cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
  Getting counts of all_measurements_cyclohexanone_mass_volume_in_urine codes for cohort all_measurements_cyclohexanone_mass_volume_in_urine
  Getting counts of all_measurements_phen_x_caffeine_protocol_050301 codes for cohort all_measurements_phen_x_caffeine_protocol_050301
  Getting counts of all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
  Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
  Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
  Getting counts of all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
  Getting counts of all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
  Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
  Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
  Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
  Getting counts of all_measurements_uroporphyrin_iii_measurement codes for cohort all_measurements_uroporphyrin_iii_measurement
  Getting counts of all_measurements_uroporphyrin_measurement codes for cohort all_measurements_uroporphyrin_measurement
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:44:27.127206
  v Summary finished, at 2026-02-23 19:44:27.416479
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:44:29.099813
  v Summary finished, at 2026-02-23 19:44:29.341799
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:44:37.616305
  v Summary finished, at 2026-02-23 19:44:38.902269
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:44:41.000161
  v Summary finished, at 2026-02-23 19:44:41.544965
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:44:55.1043
  v Summary finished, at 2026-02-23 19:44:55.357164
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:44:57.201137
  v Summary finished, at 2026-02-23 19:44:57.542954
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:05.269817
  v Summary finished, at 2026-02-23 19:45:06.658731
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:45:09.39049
  v Summary finished, at 2026-02-23 19:45:10.007366
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:22.560998
  v Summary finished, at 2026-02-23 19:45:22.895317
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:24.765996
  v Summary finished, at 2026-02-23 19:45:25.034506
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:32.365048
  v Summary finished, at 2026-02-23 19:45:33.810776
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:45:35.68846
  v Summary finished, at 2026-02-23 19:45:36.118475
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:48.460625
  v Summary finished, at 2026-02-23 19:45:48.691582
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:50.390438
  v Summary finished, at 2026-02-23 19:45:50.807456
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:45:58.480341
  v Summary finished, at 2026-02-23 19:45:59.418242
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:46:01.265983
  v Summary finished, at 2026-02-23 19:46:01.644085
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:14.807972
  v Summary finished, at 2026-02-23 19:46:15.210531
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:17.173311
  v Summary finished, at 2026-02-23 19:46:17.606593
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:27.196982
  v Summary finished, at 2026-02-23 19:46:28.432184
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:46:30.952305
  v Summary finished, at 2026-02-23 19:46:31.455499
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:46.431159
  v Summary finished, at 2026-02-23 19:46:46.946503
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:49.150989
  v Summary finished, at 2026-02-23 19:46:49.473153
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:46:58.731523
  v Summary finished, at 2026-02-23 19:47:00.109637
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:47:02.28588
  v Summary finished, at 2026-02-23 19:47:02.695393
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:47:18.736906
  v Summary finished, at 2026-02-23 19:47:19.011263
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:47:21.364586
  v Summary finished, at 2026-02-23 19:47:21.820113
  i summarising data
  i summarising cohort all_measurements_cyclohexanone_mass_volume_in_urine
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:47:31.858135
  v Summary finished, at 2026-02-23 19:47:33.424082
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:47:35.685957
  v Summary finished, at 2026-02-23 19:47:36.421271
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:47:51.209411
  v Summary finished, at 2026-02-23 19:47:51.587521
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:47:53.466707
  v Summary finished, at 2026-02-23 19:47:53.797756
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:02.78338
  v Summary finished, at 2026-02-23 19:48:03.971439
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:48:06.581062
  v Summary finished, at 2026-02-23 19:48:07.195245
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:20.135752
  v Summary finished, at 2026-02-23 19:48:20.545434
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:22.530304
  v Summary finished, at 2026-02-23 19:48:22.774595
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:30.646518
  v Summary finished, at 2026-02-23 19:48:31.816508
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:48:33.823532
  v Summary finished, at 2026-02-23 19:48:34.266693
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:47.086952
  v Summary finished, at 2026-02-23 19:48:47.333458
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:48.946414
  v Summary finished, at 2026-02-23 19:48:49.352607
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:48:57.567059
  v Summary finished, at 2026-02-23 19:48:58.568213
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:49:00.424611
  v Summary finished, at 2026-02-23 19:49:00.963726
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:12.780373
  v Summary finished, at 2026-02-23 19:49:13.209495
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:15.024696
  v Summary finished, at 2026-02-23 19:49:15.277295
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:23.46217
  v Summary finished, at 2026-02-23 19:49:24.397838
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:49:26.871777
  v Summary finished, at 2026-02-23 19:49:27.239939
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:39.816852
  v Summary finished, at 2026-02-23 19:49:40.202294
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:42.100531
  v Summary finished, at 2026-02-23 19:49:42.427154
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_iii_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:49:50.456277
  v Summary finished, at 2026-02-23 19:49:51.372175
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:49:54.205722
  v Summary finished, at 2026-02-23 19:49:54.705697
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:06.971045
  v Summary finished, at 2026-02-23 19:50:07.212519
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:09.247838
  v Summary finished, at 2026-02-23 19:50:09.658186
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:18.817381
  v Summary finished, at 2026-02-23 19:50:19.766458
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:50:21.565648
  v Summary finished, at 2026-02-23 19:50:21.940171
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:33.864252
  v Summary finished, at 2026-02-23 19:50:34.121656
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:35.807016
  v Summary finished, at 2026-02-23 19:50:36.070175
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:50:43.989194
  v Summary finished, at 2026-02-23 19:50:45.1411
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:50:47.409493
  v Summary finished, at 2026-02-23 19:50:47.979949
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:00.35538
  v Summary finished, at 2026-02-23 19:51:00.609586
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:02.623673
  v Summary finished, at 2026-02-23 19:51:02.863613
  i summarising data
  i summarising cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:10.532246
  v Summary finished, at 2026-02-23 19:51:11.57382
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:51:13.854277
  v Summary finished, at 2026-02-23 19:51:14.409578
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:28.55172
  v Summary finished, at 2026-02-23 19:51:28.802343
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:30.479669
  v Summary finished, at 2026-02-23 19:51:30.831141
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:39.885517
  v Summary finished, at 2026-02-23 19:51:41.041078
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:51:42.853822
  v Summary finished, at 2026-02-23 19:51:43.20479
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:55.986939
  v Summary finished, at 2026-02-23 19:51:56.225055
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:51:57.966901
  v Summary finished, at 2026-02-23 19:51:58.215631
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:06.369231
  v Summary finished, at 2026-02-23 19:52:07.575866
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:52:09.724943
  v Summary finished, at 2026-02-23 19:52:10.099781
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:23.522
  v Summary finished, at 2026-02-23 19:52:23.925524
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:25.521244
  v Summary finished, at 2026-02-23 19:52:25.829349
  i summarising data
  i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:33.686707
  v Summary finished, at 2026-02-23 19:52:35.019903
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:52:37.196726
  v Summary finished, at 2026-02-23 19:52:37.550294
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:50.319109
  v Summary finished, at 2026-02-23 19:52:50.553011
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:52:52.472326
  v Summary finished, at 2026-02-23 19:52:52.772408
  i summarising data
  i summarising cohort all_measurements_phen_x_caffeine_protocol_050301
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:53:01.544346
  v Summary finished, at 2026-02-23 19:53:02.783068
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:53:04.76811
  v Summary finished, at 2026-02-23 19:53:05.142105
  > Binding all diagnostic results.
  Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
  > Getting measurement records based on 1 concept.
  > Subsetting records to the subjects and timing of interest.
  > Getting time between records per person.
  Summarising timings
  i The following estimates will be calculated:
  * days_between_measurements: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:53:18.792352
  v Summary finished, at 2026-02-23 19:53:19.044116
  > Getting measurements per subject.
  i The following estimates will be calculated:
  * measurements_per_subject: min, q25, median, q75, max, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:53:20.72331
  v Summary finished, at 2026-02-23 19:53:21.026791
  i summarising data
  i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
  v summariseCharacteristics finished!
  `group` is not present in settings.
  > Summarising results - value as number.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
  ! Table is collected to memory as not all requested estimates are supported on the database side
  > Start summary of data, at 2026-02-23 19:53:30.00765
  v Summary finished, at 2026-02-23 19:53:30.972252
  > Summarising results - value as concept.
  Summarising value as number
  i The following estimates will be calculated:
  * value_as_concept_id: count, percentage
  > Start summary of data, at 2026-02-23 19:53:33.252776
  v Summary finished, at 2026-02-23 19:53:33.624546
  > Binding all diagnostic results.
  [ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
  
  ══ Skipped tests (23) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-addCodelistAttribute.R:2:3',
    'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
    'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
    'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
    'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
    'test-drugDiagnostics.R:2:3', 'test-getCohortExpectations.R:3:3',
    'test-getCohortExpectations.R:26:3', 'test-getCohortExpectations.R:61:3',
    'test-phenotypeDiagnostics.R:3:3', 'test-phenotypeDiagnostics.R:87:3',
    'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
    'test-shinyDiagnostics.R:46:3'
  • empty test (4): 'test-cohortDiagnostics.R:173:1',
    'test-cohortDiagnostics.R:177:1', 'test-cohortDiagnostics.R:181:1',
    'test-cohortDiagnostics.R:187:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-codelistDiagnostics.R:125:3'): measurementDiagnostics working ──
  Expected `... <= 5` to be TRUE.
  Differences:
  `actual`:       
  `expected`: TRUE
  
  
  [ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
  Error:
  ! Test failures.
  Execution halted