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 2026-02-18 07:35:42.278636
  v Summary finished, at 2026-02-18 07:35:42.810408
  > 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 2026-02-18 07:35:45.444476
  v Summary finished, at 2026-02-18 07:35:45.891533
  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 2026-02-18 07:35:54.285447
  v Summary finished, at 2026-02-18 07:35:55.684405
  > 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 2026-02-18 07:35:57.910895
  v Summary finished, at 2026-02-18 07:35:58.572705
  > 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 2026-02-18 07:36:23.299479
  v Summary finished, at 2026-02-18 07:36:23.65557
  > 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 2026-02-18 07:36:25.688536
  v Summary finished, at 2026-02-18 07:36:25.919404
  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 2026-02-18 07:36:34.316206
  v Summary finished, at 2026-02-18 07:36:36.039464
  > 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 2026-02-18 07:36:37.973707
  v Summary finished, at 2026-02-18 07:36:38.589367
  > 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 2026-02-18 07:38:43.620437
  v Summary finished, at 2026-02-18 07:38:43.99364
  > 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 2026-02-18 07:38:45.447147
  v Summary finished, at 2026-02-18 07:38:45.681242
  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 2026-02-18 07:38:52.253007
  v Summary finished, at 2026-02-18 07:38:53.38543
  > 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 2026-02-18 07:38:55.054298
  v Summary finished, at 2026-02-18 07:38:55.400339
  > 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 2026-02-18 07:39:08.607867
  v Summary finished, at 2026-02-18 07:39:08.983006
  > 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 2026-02-18 07:39:10.471401
  v Summary finished, at 2026-02-18 07:39:10.744506
  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 2026-02-18 07:39:18.031635
  v Summary finished, at 2026-02-18 07:39:19.20425
  > 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 2026-02-18 07:39:20.976618
  v Summary finished, at 2026-02-18 07:39:21.326056
  > 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 2026-02-18 07:39:33.348133
  v Summary finished, at 2026-02-18 07:39:33.714903
  > 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 2026-02-18 07:39:35.42565
  v Summary finished, at 2026-02-18 07:39:35.824179
  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 2026-02-18 07:39:43.351469
  v Summary finished, at 2026-02-18 07:39:44.315314
  > 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 2026-02-18 07:39:46.116723
  v Summary finished, at 2026-02-18 07:39:46.511908
  > 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 2026-02-18 07:39:59.487893
  v Summary finished, at 2026-02-18 07:39:59.928395
  > 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 2026-02-18 07:40:01.676884
  v Summary finished, at 2026-02-18 07:40:01.917923
  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 2026-02-18 07:40:08.370822
  v Summary finished, at 2026-02-18 07:40:09.438464
  > 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 2026-02-18 07:40:11.304042
  v Summary finished, at 2026-02-18 07:40:11.709425
  > 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 2026-02-18 07:40:23.805477
  v Summary finished, at 2026-02-18 07:40:24.05135
  > 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 2026-02-18 07:40:25.996181
  v Summary finished, at 2026-02-18 07:40:26.406481
  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 2026-02-18 07:40:33.971467
  v Summary finished, at 2026-02-18 07:40:34.930369
  > 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 2026-02-18 07:40:36.749591
  v Summary finished, at 2026-02-18 07:40:37.216835
  > 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 2026-02-18 07:40:48.586754
  v Summary finished, at 2026-02-18 07:40:48.869234
  > 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 2026-02-18 07:40:50.28421
  v Summary finished, at 2026-02-18 07:40:50.513985
  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 2026-02-18 07:40:59.047712
  v Summary finished, at 2026-02-18 07:41:00.599907
  > 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 2026-02-18 07:41:02.692677
  v Summary finished, at 2026-02-18 07:41:03.037365
  > 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 2026-02-18 07:41:14.818075
  v Summary finished, at 2026-02-18 07:41:15.120558
  > 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 2026-02-18 07:41:16.96829
  v Summary finished, at 2026-02-18 07:41:17.408159
  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 2026-02-18 07:41:26.262075
  v Summary finished, at 2026-02-18 07:41:27.168441
  > 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 2026-02-18 07:41:29.46484
  v Summary finished, at 2026-02-18 07:41:30.001344
  > 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 2026-02-18 07:41:42.843333
  v Summary finished, at 2026-02-18 07:41:43.156245
  > 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 2026-02-18 07:41:44.776037
  v Summary finished, at 2026-02-18 07:41:45.003332
  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 2026-02-18 07:41:53.311869
  v Summary finished, at 2026-02-18 07:41:54.58926
  > 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 2026-02-18 07:41:56.386255
  v Summary finished, at 2026-02-18 07:41:56.89731
  > 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 2026-02-18 07:42:08.270308
  v Summary finished, at 2026-02-18 07:42:08.504617
  > 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 2026-02-18 07:42:10.178336
  v Summary finished, at 2026-02-18 07:42:10.479019
  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 2026-02-18 07:42:19.750893
  v Summary finished, at 2026-02-18 07:42:20.888998
  > 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 2026-02-18 07:42:23.67067
  v Summary finished, at 2026-02-18 07:42:24.31189
  > 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 2026-02-18 07:42:37.332981
  v Summary finished, at 2026-02-18 07:42:37.610166
  > 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 2026-02-18 07:42:39.332281
  v Summary finished, at 2026-02-18 07:42:39.571607
  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 2026-02-18 07:42:46.736144
  v Summary finished, at 2026-02-18 07:42:47.826096
  > 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 2026-02-18 07:42:49.697262
  v Summary finished, at 2026-02-18 07:42:50.230151
  > 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 2026-02-18 07:43:02.879445
  v Summary finished, at 2026-02-18 07:43:03.101143
  > 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 2026-02-18 07:43:04.607444
  v Summary finished, at 2026-02-18 07:43:04.847602
  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 2026-02-18 07:43:12.583642
  v Summary finished, at 2026-02-18 07:43:13.531286
  > 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 2026-02-18 07:43:15.395126
  v Summary finished, at 2026-02-18 07:43:15.916578
  > 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 2026-02-18 07:43:27.44635
  v Summary finished, at 2026-02-18 07:43:27.732207
  > 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 2026-02-18 07:43:29.44209
  v Summary finished, at 2026-02-18 07:43:29.781693
  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 2026-02-18 07:43:37.271089
  v Summary finished, at 2026-02-18 07:43:38.206864
  > 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 2026-02-18 07:43:39.946888
  v Summary finished, at 2026-02-18 07:43:40.40456
  > 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 2026-02-18 07:43:51.320062
  v Summary finished, at 2026-02-18 07:43:51.700667
  > 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 2026-02-18 07:43:53.585621
  v Summary finished, at 2026-02-18 07:43:53.855791
  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 2026-02-18 07:44:00.69554
  v Summary finished, at 2026-02-18 07:44:01.589816
  > 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 2026-02-18 07:44:03.738324
  v Summary finished, at 2026-02-18 07:44:04.214611
  > 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 2026-02-18 07:44:15.348324
  v Summary finished, at 2026-02-18 07:44:15.584485
  > 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 2026-02-18 07:44:17.099786
  v Summary finished, at 2026-02-18 07:44:17.345825
  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 2026-02-18 07:44:25.135834
  v Summary finished, at 2026-02-18 07:44:26.122576
  > 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 2026-02-18 07:44:27.94365
  v Summary finished, at 2026-02-18 07:44:28.333427
  > 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 2026-02-18 07:44:40.971136
  v Summary finished, at 2026-02-18 07:44:41.233918
  > 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 2026-02-18 07:44:42.835905
  v Summary finished, at 2026-02-18 07:44:43.143714
  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 2026-02-18 07:44:51.050574
  v Summary finished, at 2026-02-18 07:44:52.43985
  > 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 2026-02-18 07:44:54.341324
  v Summary finished, at 2026-02-18 07:44:54.687535
  > 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 2026-02-18 07:45:05.369922
  v Summary finished, at 2026-02-18 07:45:05.626857
  > 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 2026-02-18 07:45:07.259763
  v Summary finished, at 2026-02-18 07:45:07.587287
  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 2026-02-18 07:45:15.240101
  v Summary finished, at 2026-02-18 07:45:16.292552
  > 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 2026-02-18 07:45:18.172634
  v Summary finished, at 2026-02-18 07:45:18.566161
  > 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 2026-02-18 07:45:31.030245
  v Summary finished, at 2026-02-18 07:45:31.341506
  > 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 2026-02-18 07:45:32.903131
  v Summary finished, at 2026-02-18 07:45:33.155389
  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 2026-02-18 07:45:40.646489
  v Summary finished, at 2026-02-18 07:45:41.64119
  > 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 2026-02-18 07:45:43.286447
  v Summary finished, at 2026-02-18 07:45:43.63052
  > 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 2026-02-18 07:45:54.514409
  v Summary finished, at 2026-02-18 07:45:54.89812
  > 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 2026-02-18 07:45:56.324212
  v Summary finished, at 2026-02-18 07:45:56.566326
  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 2026-02-18 07:46:03.086401
  v Summary finished, at 2026-02-18 07:46:04.068011
  > 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 2026-02-18 07:46:05.764328
  v Summary finished, at 2026-02-18 07:46:06.123829
  > 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 2026-02-18 07:46:18.214239
  v Summary finished, at 2026-02-18 07:46:18.455336
  > 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 2026-02-18 07:46:20.443056
  v Summary finished, at 2026-02-18 07:46:20.814058
  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 2026-02-18 07:46:28.340611
  v Summary finished, at 2026-02-18 07:46:29.508788
  > 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 2026-02-18 07:46:31.626438
  v Summary finished, at 2026-02-18 07:46:32.1682
  > 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 2026-02-18 07:46:44.7328
  v Summary finished, at 2026-02-18 07:46:44.979207
  > 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 2026-02-18 07:46:46.559016
  v Summary finished, at 2026-02-18 07:46:46.786763
  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 2026-02-18 07:46:54.415744
  v Summary finished, at 2026-02-18 07:46:55.48519
  > 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 2026-02-18 07:46:57.395142
  v Summary finished, at 2026-02-18 07:46:57.795671
  > 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