Running ‘testthat.R’ [10m/12m]
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 2026-02-19 19:43:04.850228
  v Summary finished, at 2026-02-19 19:43:05.195947
  > 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 2026-02-19 19:43:06.950037
  v Summary finished, at 2026-02-19 19:43:07.234029
  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 2026-02-19 19:43:14.138096
  v Summary finished, at 2026-02-19 19:43:15.3592
  > 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 2026-02-19 19:43:17.178735
  v Summary finished, at 2026-02-19 19:43:17.539438
  > 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 2026-02-19 19:43:38.168555
  v Summary finished, at 2026-02-19 19:43:38.418081
  > 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 2026-02-19 19:43:39.824105
  v Summary finished, at 2026-02-19 19:43:40.081619
  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 2026-02-19 19:43:47.431631
  v Summary finished, at 2026-02-19 19:43:48.65013
  > 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 2026-02-19 19:43:50.409262
  v Summary finished, at 2026-02-19 19:43:50.803036
  > 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 2026-02-19 19:45:56.701967
  v Summary finished, at 2026-02-19 19:45:57.087661
  > 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 2026-02-19 19:45:58.73455
  v Summary finished, at 2026-02-19 19:45:58.981571
  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 2026-02-19 19:46:08.194101
  v Summary finished, at 2026-02-19 19:46:09.281335
  > 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 2026-02-19 19:46:11.540959
  v Summary finished, at 2026-02-19 19:46:11.922388
  > 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 2026-02-19 19:46:23.8948
  v Summary finished, at 2026-02-19 19:46:24.222488
  > 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 2026-02-19 19:46:26.128179
  v Summary finished, at 2026-02-19 19:46:26.54887
  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 2026-02-19 19:46:35.254237
  v Summary finished, at 2026-02-19 19:46:36.651098
  > 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 2026-02-19 19:46:38.92582
  v Summary finished, at 2026-02-19 19:46:39.477529
  > 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 2026-02-19 19:46:52.736605
  v Summary finished, at 2026-02-19 19:46:53.14548
  > 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 2026-02-19 19:46:55.367209
  v Summary finished, at 2026-02-19 19:46:55.632783
  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 2026-02-19 19:47:03.517499
  v Summary finished, at 2026-02-19 19:47:04.658743
  > 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 2026-02-19 19:47:06.553293
  v Summary finished, at 2026-02-19 19:47:06.945154
  > 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 2026-02-19 19:47:19.466398
  v Summary finished, at 2026-02-19 19:47:19.731864
  > 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 2026-02-19 19:47:21.422485
  v Summary finished, at 2026-02-19 19:47:21.667216
  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 2026-02-19 19:47:29.61523
  v Summary finished, at 2026-02-19 19:47:30.805121
  > 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 2026-02-19 19:47:33.136755
  v Summary finished, at 2026-02-19 19:47:33.494345
  > 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 2026-02-19 19:47:45.321687
  v Summary finished, at 2026-02-19 19:47:45.672269
  > 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 2026-02-19 19:47:47.168174
  v Summary finished, at 2026-02-19 19:47:47.404964
  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 2026-02-19 19:47:55.344159
  v Summary finished, at 2026-02-19 19:47:56.403514
  > 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 2026-02-19 19:47:58.297205
  v Summary finished, at 2026-02-19 19:47:58.741549
  > 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 2026-02-19 19:48:12.018921
  v Summary finished, at 2026-02-19 19:48:12.312603
  > 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 2026-02-19 19:48:14.062523
  v Summary finished, at 2026-02-19 19:48:14.384784
  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 2026-02-19 19:48:23.635938
  v Summary finished, at 2026-02-19 19:48:24.903063
  > 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 2026-02-19 19:48:27.47616
  v Summary finished, at 2026-02-19 19:48:27.944015
  > 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 2026-02-19 19:48:41.851851
  v Summary finished, at 2026-02-19 19:48:42.332605
  > 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 2026-02-19 19:48:44.343239
  v Summary finished, at 2026-02-19 19:48:44.727324
  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 2026-02-19 19:48:53.540617
  v Summary finished, at 2026-02-19 19:48:54.493249
  > 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 2026-02-19 19:48:56.459552
  v Summary finished, at 2026-02-19 19:48:56.836563
  > 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 2026-02-19 19:49:10.173334
  v Summary finished, at 2026-02-19 19:49:10.49717
  > 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 2026-02-19 19:49:12.429661
  v Summary finished, at 2026-02-19 19:49:12.767941
  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 2026-02-19 19:49:20.083354
  v Summary finished, at 2026-02-19 19:49:21.09912
  > 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 2026-02-19 19:49:23.033935
  v Summary finished, at 2026-02-19 19:49:23.397125
  > 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 2026-02-19 19:49:36.668883
  v Summary finished, at 2026-02-19 19:49:36.919636
  > 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 2026-02-19 19:49:38.709156
  v Summary finished, at 2026-02-19 19:49:38.990119
  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 2026-02-19 19:49:46.395636
  v Summary finished, at 2026-02-19 19:49:47.390723
  > 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 2026-02-19 19:49:49.449404
  v Summary finished, at 2026-02-19 19:49:49.944602
  > 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 2026-02-19 19:50:01.610194
  v Summary finished, at 2026-02-19 19:50:01.89112
  > 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 2026-02-19 19:50:03.55174
  v Summary finished, at 2026-02-19 19:50:03.857307
  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 2026-02-19 19:50:12.259834
  v Summary finished, at 2026-02-19 19:50:13.290884
  > 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 2026-02-19 19:50:15.136493
  v Summary finished, at 2026-02-19 19:50:15.505057
  > 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 2026-02-19 19:50:27.679878
  v Summary finished, at 2026-02-19 19:50:27.917693
  > 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 2026-02-19 19:50:29.608928
  v Summary finished, at 2026-02-19 19:50:29.968785
  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 2026-02-19 19:50:38.280774
  v Summary finished, at 2026-02-19 19:50:39.208091
  > 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 2026-02-19 19:50:40.929434
  v Summary finished, at 2026-02-19 19:50:41.280756
  > 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 2026-02-19 19:50:52.992253
  v Summary finished, at 2026-02-19 19:50:53.340339
  > 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 2026-02-19 19:50:54.908659
  v Summary finished, at 2026-02-19 19:50:55.221479
  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 2026-02-19 19:51:02.471717
  v Summary finished, at 2026-02-19 19:51:03.403859
  > 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 2026-02-19 19:51:05.102544
  v Summary finished, at 2026-02-19 19:51:05.74729
  > 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 2026-02-19 19:51:18.227201
  v Summary finished, at 2026-02-19 19:51:18.621062
  > 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 2026-02-19 19:51:20.248532
  v Summary finished, at 2026-02-19 19:51:20.544668
  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 2026-02-19 19:51:28.606313
  v Summary finished, at 2026-02-19 19:51:29.624361
  > 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 2026-02-19 19:51:31.510184
  v Summary finished, at 2026-02-19 19:51:31.862361
  > 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 2026-02-19 19:51:43.228878
  v Summary finished, at 2026-02-19 19:51:43.465039
  > 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 2026-02-19 19:51:45.374223
  v Summary finished, at 2026-02-19 19:51:45.645862
  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 2026-02-19 19:51:53.795558
  v Summary finished, at 2026-02-19 19:51:54.772516
  > 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 2026-02-19 19:51:56.64515
  v Summary finished, at 2026-02-19 19:51:57.02671
  > 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 2026-02-19 19:52:08.40923
  v Summary finished, at 2026-02-19 19:52:08.642477
  > 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 2026-02-19 19:52:10.341394
  v Summary finished, at 2026-02-19 19:52:10.589938
  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 2026-02-19 19:52:18.229553
  v Summary finished, at 2026-02-19 19:52:19.47675
  > 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 2026-02-19 19:52:21.651149
  v Summary finished, at 2026-02-19 19:52:22.06451
  > 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 2026-02-19 19:52:34.132213
  v Summary finished, at 2026-02-19 19:52:34.381304
  > 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 2026-02-19 19:52:35.873656
  v Summary finished, at 2026-02-19 19:52:36.101237
  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 2026-02-19 19:52:43.547385
  v Summary finished, at 2026-02-19 19:52:44.508768
  > 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 2026-02-19 19:52:46.272816
  v Summary finished, at 2026-02-19 19:52:46.65296
  > 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 2026-02-19 19:52:57.632407
  v Summary finished, at 2026-02-19 19:52:58.015356
  > 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 2026-02-19 19:52:59.600717
  v Summary finished, at 2026-02-19 19:52:59.842779
  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 2026-02-19 19:53:08.406288
  v Summary finished, at 2026-02-19 19:53:09.353492
  > 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 2026-02-19 19:53:11.269109
  v Summary finished, at 2026-02-19 19:53:11.63747
  > 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 2026-02-19 19:53:23.703994
  v Summary finished, at 2026-02-19 19:53:24.043184
  > 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 2026-02-19 19:53:25.601799
  v Summary finished, at 2026-02-19 19:53:25.862917
  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 2026-02-19 19:53:33.709039
  v Summary finished, at 2026-02-19 19:53:34.881769
  > 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 2026-02-19 19:53:36.655129
  v Summary finished, at 2026-02-19 19:53:37.039215
  > 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 2026-02-19 19:53:49.903609
  v Summary finished, at 2026-02-19 19:53:50.1696
  > 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 2026-02-19 19:53:51.884503
  v Summary finished, at 2026-02-19 19:53:52.161492
  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 2026-02-19 19:54:01.303347
  v Summary finished, at 2026-02-19 19:54:02.80677
  > 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 2026-02-19 19:54:04.943954
  v Summary finished, at 2026-02-19 19:54:05.467631
  > 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 2026-02-19 19:54:18.374595
  v Summary finished, at 2026-02-19 19:54:18.688209
  > 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 2026-02-19 19:54:20.224002
  v Summary finished, at 2026-02-19 19:54:20.469906
  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 2026-02-19 19:54:27.941475
  v Summary finished, at 2026-02-19 19:54:28.91118
  > 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 2026-02-19 19:54:30.772727
  v Summary finished, at 2026-02-19 19:54:31.145548
  > 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