Running ‘testthat.R’ [16m/16m]
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 2026-02-17 19:02:19.942469
  v Summary finished, at 2026-02-17 19:02:20.346082
  > 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 2026-02-17 19:02:22.467873
  v Summary finished, at 2026-02-17 19:02:22.780007
  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 2026-02-17 19:02:32.85104
  v Summary finished, at 2026-02-17 19:02:34.366208
  > 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 2026-02-17 19:02:36.67675
  v Summary finished, at 2026-02-17 19:02:37.188311
  > 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 2026-02-17 19:03:05.852675
  v Summary finished, at 2026-02-17 19:03:06.255503
  > 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 2026-02-17 19:03:08.52041
  v Summary finished, at 2026-02-17 19:03:08.901068
  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 2026-02-17 19:03:19.548274
  v Summary finished, at 2026-02-17 19:03:21.149424
  > 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 2026-02-17 19:03:23.39001
  v Summary finished, at 2026-02-17 19:03:23.986214
  > 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 2026-02-17 19:06:09.855579
  v Summary finished, at 2026-02-17 19:06:10.23554
  > 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 2026-02-17 19:06:12.396744
  v Summary finished, at 2026-02-17 19:06:12.75309
  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 2026-02-17 19:06:22.853294
  v Summary finished, at 2026-02-17 19:06:24.332938
  > 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 2026-02-17 19:06:27.104036
  v Summary finished, at 2026-02-17 19:06:27.680571
  > 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 2026-02-17 19:06:44.111566
  v Summary finished, at 2026-02-17 19:06:44.478918
  > 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 2026-02-17 19:06:47.048378
  v Summary finished, at 2026-02-17 19:06:47.451078
  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 2026-02-17 19:06:57.581633
  v Summary finished, at 2026-02-17 19:06:59.03098
  > 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 2026-02-17 19:07:01.791752
  v Summary finished, at 2026-02-17 19:07:02.371296
  > 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 2026-02-17 19:07:18.794696
  v Summary finished, at 2026-02-17 19:07:19.179173
  > 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 2026-02-17 19:07:21.469312
  v Summary finished, at 2026-02-17 19:07:21.847782
  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 2026-02-17 19:07:31.931729
  v Summary finished, at 2026-02-17 19:07:33.374434
  > 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 2026-02-17 19:07:36.09904
  v Summary finished, at 2026-02-17 19:07:36.689416
  > 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 2026-02-17 19:07:53.075769
  v Summary finished, at 2026-02-17 19:07:53.491114
  > 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 2026-02-17 19:07:55.969667
  v Summary finished, at 2026-02-17 19:07:56.358041
  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 2026-02-17 19:08:06.533499
  v Summary finished, at 2026-02-17 19:08:07.930937
  > 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 2026-02-17 19:08:10.534674
  v Summary finished, at 2026-02-17 19:08:11.102276
  > 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 2026-02-17 19:08:27.214442
  v Summary finished, at 2026-02-17 19:08:27.599191
  > 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 2026-02-17 19:08:29.923114
  v Summary finished, at 2026-02-17 19:08:30.32219
  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 2026-02-17 19:08:40.651071
  v Summary finished, at 2026-02-17 19:08:42.064928
  > 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 2026-02-17 19:08:44.716289
  v Summary finished, at 2026-02-17 19:08:45.357677
  > 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 2026-02-17 19:09:01.439668
  v Summary finished, at 2026-02-17 19:09:01.820312
  > 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 2026-02-17 19:09:04.098371
  v Summary finished, at 2026-02-17 19:09:04.49205
  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 2026-02-17 19:09:14.601315
  v Summary finished, at 2026-02-17 19:09:16.053646
  > 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 2026-02-17 19:09:18.736596
  v Summary finished, at 2026-02-17 19:09:19.321692
  > 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 2026-02-17 19:09:35.149185
  v Summary finished, at 2026-02-17 19:09:35.528074
  > 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 2026-02-17 19:09:37.803187
  v Summary finished, at 2026-02-17 19:09:38.182914
  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 2026-02-17 19:09:48.162293
  v Summary finished, at 2026-02-17 19:09:49.644999
  > 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 2026-02-17 19:09:52.396948
  v Summary finished, at 2026-02-17 19:09:53.006458
  > 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 2026-02-17 19:10:09.044479
  v Summary finished, at 2026-02-17 19:10:09.407788
  > 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 2026-02-17 19:10:11.553768
  v Summary finished, at 2026-02-17 19:10:11.953022
  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 2026-02-17 19:10:21.772659
  v Summary finished, at 2026-02-17 19:10:23.119711
  > 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 2026-02-17 19:10:25.783937
  v Summary finished, at 2026-02-17 19:10:26.404861
  > 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 2026-02-17 19:10:43.326963
  v Summary finished, at 2026-02-17 19:10:43.7327
  > 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 2026-02-17 19:10:46.300207
  v Summary finished, at 2026-02-17 19:10:46.784465
  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 2026-02-17 19:10:57.928625
  v Summary finished, at 2026-02-17 19:10:59.409077
  > 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 2026-02-17 19:11:01.81373
  v Summary finished, at 2026-02-17 19:11:02.316741
  > 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 2026-02-17 19:11:18.906212
  v Summary finished, at 2026-02-17 19:11:19.312222
  > 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 2026-02-17 19:11:21.717668
  v Summary finished, at 2026-02-17 19:11:22.078714
  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 2026-02-17 19:11:32.688206
  v Summary finished, at 2026-02-17 19:11:34.308868
  > 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 2026-02-17 19:11:36.843373
  v Summary finished, at 2026-02-17 19:11:37.38442
  > 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 2026-02-17 19:11:52.951859
  v Summary finished, at 2026-02-17 19:11:53.341972
  > 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 2026-02-17 19:11:55.424893
  v Summary finished, at 2026-02-17 19:11:55.767065
  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 2026-02-17 19:12:06.37646
  v Summary finished, at 2026-02-17 19:12:07.900781
  > 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 2026-02-17 19:12:10.80207
  v Summary finished, at 2026-02-17 19:12:11.433356
  > 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 2026-02-17 19:12:28.140717
  v Summary finished, at 2026-02-17 19:12:28.508874
  > 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 2026-02-17 19:12:30.607131
  v Summary finished, at 2026-02-17 19:12:30.984202
  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 2026-02-17 19:12:42.017257
  v Summary finished, at 2026-02-17 19:12:43.438358
  > 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 2026-02-17 19:12:45.952357
  v Summary finished, at 2026-02-17 19:12:46.513977
  > 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 2026-02-17 19:13:02.267266
  v Summary finished, at 2026-02-17 19:13:02.690405
  > 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 2026-02-17 19:13:05.004121
  v Summary finished, at 2026-02-17 19:13:05.386207
  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 2026-02-17 19:13:15.54259
  v Summary finished, at 2026-02-17 19:13:16.998252
  > 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 2026-02-17 19:13:19.614658
  v Summary finished, at 2026-02-17 19:13:20.44168
  > 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 2026-02-17 19:13:35.701588
  v Summary finished, at 2026-02-17 19:13:36.037037
  > 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 2026-02-17 19:13:38.147465
  v Summary finished, at 2026-02-17 19:13:38.531132
  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 2026-02-17 19:13:48.843541
  v Summary finished, at 2026-02-17 19:13:50.260955
  > 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 2026-02-17 19:13:52.934119
  v Summary finished, at 2026-02-17 19:13:53.503865
  > 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 2026-02-17 19:14:09.37312
  v Summary finished, at 2026-02-17 19:14:09.754551
  > 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 2026-02-17 19:14:12.103301
  v Summary finished, at 2026-02-17 19:14:12.473768
  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 2026-02-17 19:14:22.958508
  v Summary finished, at 2026-02-17 19:14:24.323382
  > 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 2026-02-17 19:14:26.909133
  v Summary finished, at 2026-02-17 19:14:27.481115
  > 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 2026-02-17 19:14:43.035629
  v Summary finished, at 2026-02-17 19:14:43.409458
  > 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 2026-02-17 19:14:45.60716
  v Summary finished, at 2026-02-17 19:14:45.984166
  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 2026-02-17 19:14:56.320922
  v Summary finished, at 2026-02-17 19:14:57.691372
  > 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 2026-02-17 19:15:00.35865
  v Summary finished, at 2026-02-17 19:15:00.944541
  > 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 2026-02-17 19:15:16.719636
  v Summary finished, at 2026-02-17 19:15:17.137758
  > 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 2026-02-17 19:15:19.553144
  v Summary finished, at 2026-02-17 19:15:19.941284
  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 2026-02-17 19:15:30.221976
  v Summary finished, at 2026-02-17 19:15:31.681422
  > 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 2026-02-17 19:15:34.402144
  v Summary finished, at 2026-02-17 19:15:34.989128
  > 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 2026-02-17 19:15:50.991675
  v Summary finished, at 2026-02-17 19:15:51.372625
  > 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 2026-02-17 19:15:53.685364
  v Summary finished, at 2026-02-17 19:15:54.084388
  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 2026-02-17 19:16:04.526136
  v Summary finished, at 2026-02-17 19:16:05.94065
  > 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 2026-02-17 19:16:08.593709
  v Summary finished, at 2026-02-17 19:16:09.188031
  > 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 2026-02-17 19:16:25.527392
  v Summary finished, at 2026-02-17 19:16:25.934673
  > 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 2026-02-17 19:16:28.190488
  v Summary finished, at 2026-02-17 19:16:28.575094
  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 2026-02-17 19:16:38.707321
  v Summary finished, at 2026-02-17 19:16:40.139883
  > 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 2026-02-17 19:16:42.813794
  v Summary finished, at 2026-02-17 19:16:43.40545
  > 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 2026-02-17 19:16:59.169948
  v Summary finished, at 2026-02-17 19:16:59.557532
  > 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 2026-02-17 19:17:01.797891
  v Summary finished, at 2026-02-17 19:17:02.166061
  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 2026-02-17 19:17:12.420436
  v Summary finished, at 2026-02-17 19:17:13.802528
  > 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 2026-02-17 19:17:16.434776
  v Summary finished, at 2026-02-17 19:17:17.035446
  > 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