Running ‘testthat.R’ [413s/551s]
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 2026-02-20 14:07:58.816441
  v Summary finished, at 2026-02-20 14:07:59.220832
  > 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 2026-02-20 14:08:00.881306
  v Summary finished, at 2026-02-20 14:08:01.129075
  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 2026-02-20 14:08:08.214006
  v Summary finished, at 2026-02-20 14:08:09.254973
  > 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 2026-02-20 14:08:11.403908
  v Summary finished, at 2026-02-20 14:08:11.760084
  > 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 2026-02-20 14:08:28.141555
  v Summary finished, at 2026-02-20 14:08:28.301895
  > 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 2026-02-20 14:08:29.584514
  v Summary finished, at 2026-02-20 14:08:29.873091
  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 2026-02-20 14:08:34.84093
  v Summary finished, at 2026-02-20 14:08:35.749689
  > 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 2026-02-20 14:08:37.19209
  v Summary finished, at 2026-02-20 14:08:37.440071
  > 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 2026-02-20 14:10:08.636993
  v Summary finished, at 2026-02-20 14:10:08.796237
  > 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 2026-02-20 14:10:09.709099
  v Summary finished, at 2026-02-20 14:10:09.848165
  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 2026-02-20 14:10:14.55431
  v Summary finished, at 2026-02-20 14:10:15.327136
  > 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 2026-02-20 14:10:16.958511
  v Summary finished, at 2026-02-20 14:10:17.18134
  > 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 2026-02-20 14:10:24.430753
  v Summary finished, at 2026-02-20 14:10:24.589061
  > 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 2026-02-20 14:10:25.653813
  v Summary finished, at 2026-02-20 14:10:25.861235
  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 2026-02-20 14:10:30.996184
  v Summary finished, at 2026-02-20 14:10:31.681605
  > 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 2026-02-20 14:10:32.999414
  v Summary finished, at 2026-02-20 14:10:33.25649
  > 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 2026-02-20 14:10:41.065266
  v Summary finished, at 2026-02-20 14:10:41.225098
  > 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 2026-02-20 14:10:42.706612
  v Summary finished, at 2026-02-20 14:10:42.891143
  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 2026-02-20 14:10:47.668379
  v Summary finished, at 2026-02-20 14:10:48.268607
  > 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 2026-02-20 14:10:49.717311
  v Summary finished, at 2026-02-20 14:10:50.052758
  > 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 2026-02-20 14:10:59.434126
  v Summary finished, at 2026-02-20 14:10:59.774885
  > 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 2026-02-20 14:11:00.846754
  v Summary finished, at 2026-02-20 14:11:01.017497
  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 2026-02-20 14:11:07.402021
  v Summary finished, at 2026-02-20 14:11:08.157278
  > 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 2026-02-20 14:11:09.284541
  v Summary finished, at 2026-02-20 14:11:09.543294
  > 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 2026-02-20 14:11:18.578187
  v Summary finished, at 2026-02-20 14:11:18.764655
  > 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 2026-02-20 14:11:19.965781
  v Summary finished, at 2026-02-20 14:11:20.298619
  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 2026-02-20 14:11:27.085201
  v Summary finished, at 2026-02-20 14:11:27.813029
  > 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 2026-02-20 14:11:29.765394
  v Summary finished, at 2026-02-20 14:11:30.254269
  > 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 2026-02-20 14:11:40.938694
  v Summary finished, at 2026-02-20 14:11:41.103945
  > 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 2026-02-20 14:11:42.086241
  v Summary finished, at 2026-02-20 14:11:42.326622
  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 2026-02-20 14:11:47.699729
  v Summary finished, at 2026-02-20 14:11:48.66401
  > 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 2026-02-20 14:11:49.970345
  v Summary finished, at 2026-02-20 14:11:50.202468
  > 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 2026-02-20 14:11:58.575325
  v Summary finished, at 2026-02-20 14:11:58.746571
  > 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 2026-02-20 14:11:59.772038
  v Summary finished, at 2026-02-20 14:11:59.953483
  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 2026-02-20 14:12:05.489538
  v Summary finished, at 2026-02-20 14:12:06.182356
  > 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 2026-02-20 14:12:07.323694
  v Summary finished, at 2026-02-20 14:12:07.616919
  > 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 2026-02-20 14:12:16.934773
  v Summary finished, at 2026-02-20 14:12:17.445947
  > 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 2026-02-20 14:12:18.350757
  v Summary finished, at 2026-02-20 14:12:18.551981
  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 2026-02-20 14:12:24.825025
  v Summary finished, at 2026-02-20 14:12:25.391885
  > 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 2026-02-20 14:12:26.444149
  v Summary finished, at 2026-02-20 14:12:26.711634
  > 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 2026-02-20 14:12:34.112097
  v Summary finished, at 2026-02-20 14:12:34.348132
  > 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 2026-02-20 14:12:35.283205
  v Summary finished, at 2026-02-20 14:12:35.422877
  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 2026-02-20 14:12:40.395368
  v Summary finished, at 2026-02-20 14:12:40.992516
  > 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 2026-02-20 14:12:42.270827
  v Summary finished, at 2026-02-20 14:12:42.52269
  > 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 2026-02-20 14:12:50.750199
  v Summary finished, at 2026-02-20 14:12:50.965598
  > 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 2026-02-20 14:12:51.856031
  v Summary finished, at 2026-02-20 14:12:52.007405
  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 2026-02-20 14:12:57.18245
  v Summary finished, at 2026-02-20 14:12:58.000098
  > 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 2026-02-20 14:12:59.782231
  v Summary finished, at 2026-02-20 14:13:00.125496
  > 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 2026-02-20 14:13:09.34742
  v Summary finished, at 2026-02-20 14:13:09.598761
  > 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 2026-02-20 14:13:10.516265
  v Summary finished, at 2026-02-20 14:13:10.672056
  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 2026-02-20 14:13:15.865926
  v Summary finished, at 2026-02-20 14:13:16.54931
  > 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 2026-02-20 14:13:17.911169
  v Summary finished, at 2026-02-20 14:13:18.402799
  > 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 2026-02-20 14:13:28.436209
  v Summary finished, at 2026-02-20 14:13:28.702061
  > 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 2026-02-20 14:13:29.987833
  v Summary finished, at 2026-02-20 14:13:30.175254
  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 2026-02-20 14:13:37.680444
  v Summary finished, at 2026-02-20 14:13:38.627919
  > 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 2026-02-20 14:13:39.975915
  v Summary finished, at 2026-02-20 14:13:40.381792
  > 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 2026-02-20 14:13:50.283213
  v Summary finished, at 2026-02-20 14:13:50.573795
  > 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 2026-02-20 14:13:51.809751
  v Summary finished, at 2026-02-20 14:13:51.983281
  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 2026-02-20 14:13:58.419217
  v Summary finished, at 2026-02-20 14:13:59.346384
  > 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 2026-02-20 14:14:01.266817
  v Summary finished, at 2026-02-20 14:14:01.822127
  > 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 2026-02-20 14:14:15.041074
  v Summary finished, at 2026-02-20 14:14:15.336605
  > 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 2026-02-20 14:14:16.618048
  v Summary finished, at 2026-02-20 14:14:17.00242
  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 2026-02-20 14:14:22.830847
  v Summary finished, at 2026-02-20 14:14:23.726984
  > 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 2026-02-20 14:14:25.445255
  v Summary finished, at 2026-02-20 14:14:25.733029
  > 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 2026-02-20 14:14:35.792423
  v Summary finished, at 2026-02-20 14:14:35.952274
  > 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 2026-02-20 14:14:37.535808
  v Summary finished, at 2026-02-20 14:14:37.930777
  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 2026-02-20 14:14:44.95093
  v Summary finished, at 2026-02-20 14:14:45.702185
  > 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 2026-02-20 14:14:47.405324
  v Summary finished, at 2026-02-20 14:14:47.661895
  > 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 2026-02-20 14:14:58.02245
  v Summary finished, at 2026-02-20 14:14:58.433306
  > 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 2026-02-20 14:15:00.509019
  v Summary finished, at 2026-02-20 14:15:00.750806
  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 2026-02-20 14:15:07.727686
  v Summary finished, at 2026-02-20 14:15:08.773569
  > 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 2026-02-20 14:15:10.543463
  v Summary finished, at 2026-02-20 14:15:10.773951
  > 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 2026-02-20 14:15:21.560828
  v Summary finished, at 2026-02-20 14:15:21.789606
  > 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 2026-02-20 14:15:22.96937
  v Summary finished, at 2026-02-20 14:15:23.230319
  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 2026-02-20 14:15:29.130656
  v Summary finished, at 2026-02-20 14:15:29.873108
  > 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 2026-02-20 14:15:30.997736
  v Summary finished, at 2026-02-20 14:15:31.25326
  > 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 2026-02-20 14:15:39.927636
  v Summary finished, at 2026-02-20 14:15:40.117432
  > 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 2026-02-20 14:15:41.741193
  v Summary finished, at 2026-02-20 14:15:41.967147
  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 2026-02-20 14:15:47.130837
  v Summary finished, at 2026-02-20 14:15:47.93573
  > 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 2026-02-20 14:15:49.690238
  v Summary finished, at 2026-02-20 14:15:49.938817
  > 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 2026-02-20 14:15:58.169222
  v Summary finished, at 2026-02-20 14:15:58.442708
  > 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 2026-02-20 14:15:59.719311
  v Summary finished, at 2026-02-20 14:16:00.000499
  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 2026-02-20 14:16:07.248749
  v Summary finished, at 2026-02-20 14:16:08.087743
  > 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 2026-02-20 14:16:10.059757
  v Summary finished, at 2026-02-20 14:16:10.379625
  > 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 2026-02-20 14:16:20.028028
  v Summary finished, at 2026-02-20 14:16:20.380563
  > 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 2026-02-20 14:16:21.963686
  v Summary finished, at 2026-02-20 14:16:22.169167
  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 2026-02-20 14:16:28.452317
  v Summary finished, at 2026-02-20 14:16:29.362799
  > 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 2026-02-20 14:16:30.645421
  v Summary finished, at 2026-02-20 14:16:30.87032
  > 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