Last updated on 2026-02-19 11:54:16 CET.
| Package | ERROR | OK |
|---|---|---|
| CodelistGenerator | 1 | 13 |
| CohortConstructor | 1 | 13 |
| IncidencePrevalence | 14 | |
| OmopOnSpark | 14 | |
| PhenotypeR | 5 | 9 |
Current CRAN status: ERROR: 1, OK: 13
Version: 4.0.2
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘PatientProfiles’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 13
Version: 0.6.1
Check: package dependencies
Result: ERROR
Packages required and available but unsuitable versions:
'PatientProfiles', 'CodelistGenerator'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: ERROR: 5, OK: 9
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [438s/578s]
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 14:07:41.985283
v Summary finished, at 2026-02-18 14:07:42.230043
> 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 14:07:43.876962
v Summary finished, at 2026-02-18 14:07:44.167255
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 14:07:51.280389
v Summary finished, at 2026-02-18 14:07:52.805624
> 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 14:07:54.60469
v Summary finished, at 2026-02-18 14:07:54.959297
> 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 14:08:09.648846
v Summary finished, at 2026-02-18 14:08:09.858762
> 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 14:08:11.473412
v Summary finished, at 2026-02-18 14:08:11.738229
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 14:08:18.255371
v Summary finished, at 2026-02-18 14:08:19.137558
> 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 14:08:20.920362
v Summary finished, at 2026-02-18 14:08:21.1703
> 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 14:09:58.22143
v Summary finished, at 2026-02-18 14:09:58.39389
> 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 14:09:59.588978
v Summary finished, at 2026-02-18 14:09:59.770763
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 14:10:05.187559
v Summary finished, at 2026-02-18 14:10:05.854688
> 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 14:10:07.390233
v Summary finished, at 2026-02-18 14:10:07.858492
> 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 14:10:16.524169
v Summary finished, at 2026-02-18 14:10:16.75763
> 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 14:10:17.785461
v Summary finished, at 2026-02-18 14:10:17.956491
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 14:10:23.043196
v Summary finished, at 2026-02-18 14:10:23.858078
> 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 14:10:25.601625
v Summary finished, at 2026-02-18 14:10:26.077965
> 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 14:10:35.60429
v Summary finished, at 2026-02-18 14:10:35.775172
> 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 14:10:36.679099
v Summary finished, at 2026-02-18 14:10:36.840425
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 14:10:42.446757
v Summary finished, at 2026-02-18 14:10:43.04557
> 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 14:10:44.234293
v Summary finished, at 2026-02-18 14:10:44.483735
> 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 14:10:55.545975
v Summary finished, at 2026-02-18 14:10:55.86261
> 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 14:10:57.216523
v Summary finished, at 2026-02-18 14:10:57.375759
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 14:11:03.283535
v Summary finished, at 2026-02-18 14:11:03.924363
> 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 14:11:05.403854
v Summary finished, at 2026-02-18 14:11:05.757864
> 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 14:11:14.737308
v Summary finished, at 2026-02-18 14:11:14.908604
> 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 14:11:16.105231
v Summary finished, at 2026-02-18 14:11:16.286709
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 14:11:21.161425
v Summary finished, at 2026-02-18 14:11:21.933594
> 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 14:11:23.244135
v Summary finished, at 2026-02-18 14:11:23.644958
> 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 14:11:33.813127
v Summary finished, at 2026-02-18 14:11:33.997033
> 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 14:11:35.210889
v Summary finished, at 2026-02-18 14:11:35.406658
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 14:11:40.869155
v Summary finished, at 2026-02-18 14:11:41.503766
> 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 14:11:42.805839
v Summary finished, at 2026-02-18 14:11:43.210703
> 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 14:11:52.729469
v Summary finished, at 2026-02-18 14:11:52.896288
> 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 14:11:54.209605
v Summary finished, at 2026-02-18 14:11:54.380328
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 14:11:59.732343
v Summary finished, at 2026-02-18 14:12:00.805318
> 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 14:12:02.069218
v Summary finished, at 2026-02-18 14:12:02.303927
> 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 14:12:12.294249
v Summary finished, at 2026-02-18 14:12:12.565999
> 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 14:12:13.838189
v Summary finished, at 2026-02-18 14:12:14.035782
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 14:12:20.824423
v Summary finished, at 2026-02-18 14:12:21.395489
> 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 14:12:22.757323
v Summary finished, at 2026-02-18 14:12:23.020257
> 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 14:12:32.248629
v Summary finished, at 2026-02-18 14:12:32.380049
> 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 14:12:33.660636
v Summary finished, at 2026-02-18 14:12:33.898343
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 14:12:39.898199
v Summary finished, at 2026-02-18 14:12:40.623248
> 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 14:12:42.530929
v Summary finished, at 2026-02-18 14:12:42.998042
> 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 14:12:53.22255
v Summary finished, at 2026-02-18 14:12:53.479608
> 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 14:12:54.918921
v Summary finished, at 2026-02-18 14:12:55.265465
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 14:13:01.088233
v Summary finished, at 2026-02-18 14:13:01.717847
> 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 14:13:03.430362
v Summary finished, at 2026-02-18 14:13:03.786491
> 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 14:13:13.18868
v Summary finished, at 2026-02-18 14:13:13.510275
> 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 14:13:14.992092
v Summary finished, at 2026-02-18 14:13:15.238923
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 14:13:20.763684
v Summary finished, at 2026-02-18 14:13:21.470935
> 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 14:13:23.476434
v Summary finished, at 2026-02-18 14:13:23.867218
> 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 14:13:35.901408
v Summary finished, at 2026-02-18 14:13:36.183729
> 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 14:13:37.629333
v Summary finished, at 2026-02-18 14:13:37.967329
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 14:13:45.401929
v Summary finished, at 2026-02-18 14:13:46.098321
> 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 14:13:47.36596
v Summary finished, at 2026-02-18 14:13:47.630593
> 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 14:13:58.046319
v Summary finished, at 2026-02-18 14:13:58.39445
> 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 14:13:59.836023
v Summary finished, at 2026-02-18 14:14:00.003982
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 14:14:07.403242
v Summary finished, at 2026-02-18 14:14:08.3819
> 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 14:14:09.908279
v Summary finished, at 2026-02-18 14:14:10.182247
> 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 14:14:19.747562
v Summary finished, at 2026-02-18 14:14:19.975491
> 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 14:14:21.351171
v Summary finished, at 2026-02-18 14:14:21.530077
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 14:14:27.333645
v Summary finished, at 2026-02-18 14:14:28.038652
> 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 14:14:29.085788
v Summary finished, at 2026-02-18 14:14:29.470507
> 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 14:14:38.158142
v Summary finished, at 2026-02-18 14:14:38.337388
> 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 14:14:39.694455
v Summary finished, at 2026-02-18 14:14:39.91066
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 14:14:45.835502
v Summary finished, at 2026-02-18 14:14:46.532209
> 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 14:14:47.816772
v Summary finished, at 2026-02-18 14:14:48.058141
> 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 14:14:58.96189
v Summary finished, at 2026-02-18 14:14:59.219625
> 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 14:15:00.416412
v Summary finished, at 2026-02-18 14:15:00.570549
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 14:15:06.329574
v Summary finished, at 2026-02-18 14:15:07.049174
> 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 14:15:08.36522
v Summary finished, at 2026-02-18 14:15:08.706078
> 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 14:15:18.973796
v Summary finished, at 2026-02-18 14:15:19.171479
> 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 14:15:21.005141
v Summary finished, at 2026-02-18 14:15:21.411099
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 14:15:27.816742
v Summary finished, at 2026-02-18 14:15:28.513381
> 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 14:15:30.353142
v Summary finished, at 2026-02-18 14:15:30.641604
> 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 14:15:41.899374
v Summary finished, at 2026-02-18 14:15:42.186113
> 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 14:15:43.925011
v Summary finished, at 2026-02-18 14:15:44.296118
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 14:15:51.607741
v Summary finished, at 2026-02-18 14:15:52.972464
> 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 14:15:55.081662
v Summary finished, at 2026-02-18 14:15:55.45175
> 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 14:16:05.620881
v Summary finished, at 2026-02-18 14:16:06.039878
> 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 14:16:07.683265
v Summary finished, at 2026-02-18 14:16:07.851125
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 14:16:14.854378
v Summary finished, at 2026-02-18 14:16:15.642214
> 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 14:16:17.274513
v Summary finished, at 2026-02-18 14:16:17.641356
> 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 14:16:27.514554
v Summary finished, at 2026-02-18 14:16:27.82076
> 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 14:16:28.758039
v Summary finished, at 2026-02-18 14:16:28.915025
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 14:16:35.894555
v Summary finished, at 2026-02-18 14:16:36.572143
> 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 14:16:37.780117
v Summary finished, at 2026-02-18 14:16:38.076795
> 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [16m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PhenotypeR)
>
> test_check("PhenotypeR")
Creating a new cdm
Uploading table person (100 rows) - [1/13]
Uploading table observation_period (100 rows) - [2/13]
Uploading table cdm_source (1 rows) - [3/13]
Uploading table concept (3361 rows) - [4/13]
Uploading table vocabulary (65 rows) - [5/13]
Uploading table concept_relationship (117257 rows) - [6/13]
Uploading table concept_synonym (3895 rows) - [7/13]
Uploading table concept_ancestor (1327 rows) - [8/13]
Uploading table drug_strength (45 rows) - [9/13]
Uploading table condition_occurrence (600 rows) - [10/13]
Uploading table drug_exposure (3100 rows) - [11/13]
Uploading table measurement (2000 rows) - [12/13]
Uploading table my_cohort_1 (100 rows) - [13/13]
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_cohort created.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:19.942469
v Summary finished, at 2026-02-17 19:02:20.346082
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:22.467873
v Summary finished, at 2026-02-17 19:02:22.780007
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:32.85104
v Summary finished, at 2026-02-17 19:02:34.366208
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:02:36.67675
v Summary finished, at 2026-02-17 19:02:37.188311
> Binding all diagnostic results.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:05.852675
v Summary finished, at 2026-02-17 19:03:06.255503
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:08.52041
v Summary finished, at 2026-02-17 19:03:08.901068
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:19.548274
v Summary finished, at 2026-02-17 19:03:21.149424
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:03:23.39001
v Summary finished, at 2026-02-17 19:03:23.986214
> Binding all diagnostic results.
Saving _problems/test-codelistDiagnostics-129.R
Getting counts of all_measurements codes for cohort all_measurements
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_2 created.
Getting counts of all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
Getting counts of all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_isoenzymes_measurement codes for cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
Getting counts of all_measurements_cyclohexanone_mass_volume_in_urine codes for cohort all_measurements_cyclohexanone_mass_volume_in_urine
Getting counts of all_measurements_phen_x_caffeine_protocol_050301 codes for cohort all_measurements_phen_x_caffeine_protocol_050301
Getting counts of all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
Getting counts of all_measurements_uroporphyrin_iii_measurement codes for cohort all_measurements_uroporphyrin_iii_measurement
Getting counts of all_measurements_uroporphyrin_measurement codes for cohort all_measurements_uroporphyrin_measurement
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:09.855579
v Summary finished, at 2026-02-17 19:06:10.23554
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:12.396744
v Summary finished, at 2026-02-17 19:06:12.75309
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:22.853294
v Summary finished, at 2026-02-17 19:06:24.332938
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:06:27.104036
v Summary finished, at 2026-02-17 19:06:27.680571
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:44.111566
v Summary finished, at 2026-02-17 19:06:44.478918
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:47.048378
v Summary finished, at 2026-02-17 19:06:47.451078
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:57.581633
v Summary finished, at 2026-02-17 19:06:59.03098
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:07:01.791752
v Summary finished, at 2026-02-17 19:07:02.371296
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:18.794696
v Summary finished, at 2026-02-17 19:07:19.179173
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:21.469312
v Summary finished, at 2026-02-17 19:07:21.847782
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:31.931729
v Summary finished, at 2026-02-17 19:07:33.374434
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:07:36.09904
v Summary finished, at 2026-02-17 19:07:36.689416
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:53.075769
v Summary finished, at 2026-02-17 19:07:53.491114
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:55.969667
v Summary finished, at 2026-02-17 19:07:56.358041
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:06.533499
v Summary finished, at 2026-02-17 19:08:07.930937
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:08:10.534674
v Summary finished, at 2026-02-17 19:08:11.102276
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:27.214442
v Summary finished, at 2026-02-17 19:08:27.599191
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:29.923114
v Summary finished, at 2026-02-17 19:08:30.32219
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:40.651071
v Summary finished, at 2026-02-17 19:08:42.064928
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:08:44.716289
v Summary finished, at 2026-02-17 19:08:45.357677
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:01.439668
v Summary finished, at 2026-02-17 19:09:01.820312
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:04.098371
v Summary finished, at 2026-02-17 19:09:04.49205
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:14.601315
v Summary finished, at 2026-02-17 19:09:16.053646
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:09:18.736596
v Summary finished, at 2026-02-17 19:09:19.321692
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:35.149185
v Summary finished, at 2026-02-17 19:09:35.528074
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:37.803187
v Summary finished, at 2026-02-17 19:09:38.182914
i summarising data
i summarising cohort all_measurements_cyclohexanone_mass_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:48.162293
v Summary finished, at 2026-02-17 19:09:49.644999
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:09:52.396948
v Summary finished, at 2026-02-17 19:09:53.006458
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:09.044479
v Summary finished, at 2026-02-17 19:10:09.407788
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:11.553768
v Summary finished, at 2026-02-17 19:10:11.953022
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:21.772659
v Summary finished, at 2026-02-17 19:10:23.119711
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:10:25.783937
v Summary finished, at 2026-02-17 19:10:26.404861
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:43.326963
v Summary finished, at 2026-02-17 19:10:43.7327
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:46.300207
v Summary finished, at 2026-02-17 19:10:46.784465
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:57.928625
v Summary finished, at 2026-02-17 19:10:59.409077
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:11:01.81373
v Summary finished, at 2026-02-17 19:11:02.316741
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:18.906212
v Summary finished, at 2026-02-17 19:11:19.312222
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:21.717668
v Summary finished, at 2026-02-17 19:11:22.078714
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:32.688206
v Summary finished, at 2026-02-17 19:11:34.308868
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:11:36.843373
v Summary finished, at 2026-02-17 19:11:37.38442
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:52.951859
v Summary finished, at 2026-02-17 19:11:53.341972
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:55.424893
v Summary finished, at 2026-02-17 19:11:55.767065
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:06.37646
v Summary finished, at 2026-02-17 19:12:07.900781
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:12:10.80207
v Summary finished, at 2026-02-17 19:12:11.433356
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:28.140717
v Summary finished, at 2026-02-17 19:12:28.508874
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:30.607131
v Summary finished, at 2026-02-17 19:12:30.984202
i summarising data
i summarising cohort all_measurements_uroporphyrin_iii_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:42.017257
v Summary finished, at 2026-02-17 19:12:43.438358
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:12:45.952357
v Summary finished, at 2026-02-17 19:12:46.513977
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:02.267266
v Summary finished, at 2026-02-17 19:13:02.690405
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:05.004121
v Summary finished, at 2026-02-17 19:13:05.386207
i summarising data
i summarising cohort all_measurements_uroporphyrin_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:15.54259
v Summary finished, at 2026-02-17 19:13:16.998252
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:13:19.614658
v Summary finished, at 2026-02-17 19:13:20.44168
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:35.701588
v Summary finished, at 2026-02-17 19:13:36.037037
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:38.147465
v Summary finished, at 2026-02-17 19:13:38.531132
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:48.843541
v Summary finished, at 2026-02-17 19:13:50.260955
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:13:52.934119
v Summary finished, at 2026-02-17 19:13:53.503865
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:09.37312
v Summary finished, at 2026-02-17 19:14:09.754551
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:12.103301
v Summary finished, at 2026-02-17 19:14:12.473768
i summarising data
i summarising cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:22.958508
v Summary finished, at 2026-02-17 19:14:24.323382
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:14:26.909133
v Summary finished, at 2026-02-17 19:14:27.481115
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:43.035629
v Summary finished, at 2026-02-17 19:14:43.409458
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:45.60716
v Summary finished, at 2026-02-17 19:14:45.984166
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:56.320922
v Summary finished, at 2026-02-17 19:14:57.691372
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:15:00.35865
v Summary finished, at 2026-02-17 19:15:00.944541
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:16.719636
v Summary finished, at 2026-02-17 19:15:17.137758
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:19.553144
v Summary finished, at 2026-02-17 19:15:19.941284
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:30.221976
v Summary finished, at 2026-02-17 19:15:31.681422
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:15:34.402144
v Summary finished, at 2026-02-17 19:15:34.989128
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:50.991675
v Summary finished, at 2026-02-17 19:15:51.372625
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:53.685364
v Summary finished, at 2026-02-17 19:15:54.084388
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:04.526136
v Summary finished, at 2026-02-17 19:16:05.94065
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:16:08.593709
v Summary finished, at 2026-02-17 19:16:09.188031
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:25.527392
v Summary finished, at 2026-02-17 19:16:25.934673
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:28.190488
v Summary finished, at 2026-02-17 19:16:28.575094
i summarising data
i summarising cohort all_measurements_phen_x_caffeine_protocol_050301
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:38.707321
v Summary finished, at 2026-02-17 19:16:40.139883
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:16:42.813794
v Summary finished, at 2026-02-17 19:16:43.40545
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:59.169948
v Summary finished, at 2026-02-17 19:16:59.557532
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:17:01.797891
v Summary finished, at 2026-02-17 19:17:02.166061
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:17:12.420436
v Summary finished, at 2026-02-17 19:17:13.802528
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:17:16.434776
v Summary finished, at 2026-02-17 19:17:17.035446
> Binding all diagnostic results.
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
══ Skipped tests (23) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-addCodelistAttribute.R:2:3',
'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
'test-drugDiagnostics.R:2:3', 'test-getCohortExpectations.R:3:3',
'test-getCohortExpectations.R:26:3', 'test-getCohortExpectations.R:61:3',
'test-phenotypeDiagnostics.R:3:3', 'test-phenotypeDiagnostics.R:87:3',
'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
'test-shinyDiagnostics.R:46:3'
• empty test (4): 'test-cohortDiagnostics.R:173:1',
'test-cohortDiagnostics.R:177:1', 'test-cohortDiagnostics.R:181:1',
'test-cohortDiagnostics.R:187:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-codelistDiagnostics.R:125:3'): measurementDiagnostics working ──
Expected `... <= 5` to be TRUE.
Differences:
`actual`:
`expected`: TRUE
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17m/48m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PhenotypeR)
>
> test_check("PhenotypeR")
Creating a new cdm
Uploading table person (100 rows) - [1/13]
Uploading table observation_period (100 rows) - [2/13]
Uploading table cdm_source (1 rows) - [3/13]
Uploading table concept (3361 rows) - [4/13]
Uploading table vocabulary (65 rows) - [5/13]
Uploading table concept_relationship (117257 rows) - [6/13]
Uploading table concept_synonym (3895 rows) - [7/13]
Uploading table concept_ancestor (1327 rows) - [8/13]
Uploading table drug_strength (45 rows) - [9/13]
Uploading table condition_occurrence (600 rows) - [10/13]
Uploading table drug_exposure (3100 rows) - [11/13]
Uploading table measurement (2000 rows) - [12/13]
Uploading table my_cohort_1 (100 rows) - [13/13]
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_cohort created.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:19:32.437344
v Summary finished, at 2026-02-17 17:19:33.811444
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:19:43.756279
v Summary finished, at 2026-02-17 17:19:45.040758
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:20:17.717471
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:20:25.46774
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:20:35.929764
v Summary finished, at 2026-02-17 17:20:38.331205
> Binding all diagnostic results.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:21:55.632436
v Summary finished, at 2026-02-17 17:21:56.619268
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:22:07.281538
v Summary finished, at 2026-02-17 17:22:08.419101
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:22:39.303519
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:22:47.780271
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:23:04.028065
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:23:07.247178
> Binding all diagnostic results.
Saving _problems/test-codelistDiagnostics-129.R
Getting counts of all_measurements codes for cohort all_measurements
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_2 created.
Getting counts of all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
Getting counts of all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_isoenzymes_measurement codes for cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
Getting counts of all_measurements_cyclohexanone_mass_volume_in_urine codes for cohort all_measurements_cyclohexanone_mass_volume_in_urine
Getting counts of all_measurements_phen_x_caffeine_protocol_050301 codes for cohort all_measurements_phen_x_caffeine_protocol_050301
Getting counts of all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
Getting counts of all_measurements_uroporphyrin_iii_measurement codes for cohort all_measurements_uroporphyrin_iii_measurement
Getting counts of all_measurements_uroporphyrin_measurement codes for cohort all_measurements_uroporphyrin_measurement
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:32:25.047052
v Summary finished, at 2026-02-17 17:32:26.663556
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:32:37.049485
v Summary finished, at 2026-02-17 17:32:38.986975
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:33:25.531442
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:33:32.496655
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:33:42.07422
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:33:44.800601
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:34:27.71252
v Summary finished, at 2026-02-17 17:34:30.021218
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:34:39.939659
v Summary finished, at 2026-02-17 17:34:40.398309
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:35:26.033876
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:35:32.635724
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:35:41.838229
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:35:43.706217
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:36:25.366606
v Summary finished, at 2026-02-17 17:36:26.858542
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:36:35.120296
v Summary finished, at 2026-02-17 17:36:36.423248
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:37:17.089879
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:37:21.8805
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:37:35.106432
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:37:37.554662
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:38:33.580334
v Summary finished, at 2026-02-17 17:38:35.040456
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:38:45.005094
v Summary finished, at 2026-02-17 17:38:46.203275
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:39:15.496118
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:39:20.419325
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:39:31.772235
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:39:34.04124
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:40:30.893179
v Summary finished, at 2026-02-17 17:40:32.818675
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:40:44.941265
v Summary finished, at 2026-02-17 17:40:46.409181
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:41:26.97677
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:41:33.644988
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:41:45.438314
v Summary finished, at 2026-02-17 17:41:48.214741
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:42:40.715773
v Summary finished, at 2026-02-17 17:42:42.611387
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:42:51.539685
v Summary finished, at 2026-02-17 17:42:52.81315
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:43:30.949866
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:43:38.114868
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:43:51.897787
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:43:54.437541
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:02.088213
v Summary finished, at 2026-02-17 17:45:03.712452
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:11.918732
v Summary finished, at 2026-02-17 17:45:13.540194
i summarising data
i summarising cohort all_measurements_cyclohexanone_mass_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:53.149677
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:45:59.385087
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:46:14.015355
v Summary finished, at 2026-02-17 17:46:15.48819
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:08.307702
v Summary finished, at 2026-02-17 17:47:08.840982
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:18.514693
v Summary finished, at 2026-02-17 17:47:19.93769
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:47.021247
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:47:50.822719
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:47:55.878247
v Summary finished, at 2026-02-17 17:47:58.30402
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:48:31.424
v Summary finished, at 2026-02-17 17:48:32.080838
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:48:37.221476
v Summary finished, at 2026-02-17 17:48:38.850511
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:06.241469
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:49:08.717035
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:49:15.166657
v Summary finished, at 2026-02-17 17:49:16.688111
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:48.544702
v Summary finished, at 2026-02-17 17:49:49.547263
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:54.85452
v Summary finished, at 2026-02-17 17:49:56.84437
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:50:21.955356
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:50:28.643666
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:50:43.294499
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:50:46.531879
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:51:34.367851
v Summary finished, at 2026-02-17 17:51:34.790582
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:51:41.953669
v Summary finished, at 2026-02-17 17:51:42.303404
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:09.463512
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:52:11.793239
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:52:15.637428
v Summary finished, at 2026-02-17 17:52:16.685729
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:46.387237
v Summary finished, at 2026-02-17 17:52:47.245592
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:53.537087
v Summary finished, at 2026-02-17 17:52:54.543273
i summarising data
i summarising cohort all_measurements_uroporphyrin_iii_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:53:22.511507
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:53:29.584009
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:53:37.034934
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:53:39.622445
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:54:29.401701
v Summary finished, at 2026-02-17 17:54:30.615729
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:54:36.850435
v Summary finished, at 2026-02-17 17:54:38.210499
i summarising data
i summarising cohort all_measurements_uroporphyrin_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:08.64764
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:55:12.706535
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:55:20.563302
v Summary finished, at 2026-02-17 17:55:22.219533
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:44.461745
v Summary finished, at 2026-02-17 17:55:44.932321
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:52.541106
v Summary finished, at 2026-02-17 17:55:53.674622
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:56:16.68461
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:56:20.857003
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:56:27.038719
v Summary finished, at 2026-02-17 17:56:28.380227
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:56:57.674801
v Summary finished, at 2026-02-17 17:56:58.848567
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:57:07.525557
v Summary finished, at 2026-02-17 17:57:08.88763
i summarising data
i summarising cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:57:35.943478
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:57:38.336685
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:57:43.349699
v Summary finished, at 2026-02-17 17:57:44.871527
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:10.461081
v Summary finished, at 2026-02-17 17:58:11.169447
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:16.650083
v Summary finished, at 2026-02-17 17:58:17.149279
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:38.891564
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:58:44.540419
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:58:53.555989
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:58:56.237386
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:59:36.158056
v Summary finished, at 2026-02-17 17:59:38.611523
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:59:44.021942
v Summary finished, at 2026-02-17 17:59:44.493247
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:07.672033
v Summary finished, at 2026-02-17 18:00:11.511974
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:00:18.194567
v Summary finished, at 2026-02-17 18:00:19.685022
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:52.525363
v Summary finished, at 2026-02-17 18:00:53.247886
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:58.903271
v Summary finished, at 2026-02-17 18:00:59.668282
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:20.305136
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:01:23.490053
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:01:28.473849
v Summary finished, at 2026-02-17 18:01:30.245683
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:52.397255
v Summary finished, at 2026-02-17 18:01:53.243902
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:57.884329
v Summary finished, at 2026-02-17 18:01:58.951531
i summarising data
i summarising cohort all_measurements_phen_x_caffeine_protocol_050301
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:02:15.228605
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:02:18.447197
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:02:27.244568
v Summary finished, at 2026-02-17 18:02:29.167581
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:02:58.998619
v Summary finished, at 2026-02-17 18:03:01.110648
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:03:12.609736
v Summary finished, at 2026-02-17 18:03:13.795691
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:03:38.27593
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:03:42.242708
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:03:49.245941
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:03:52.852519
> 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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.3.2
Check: tests
Result: ERROR
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
Flavor: r-patched-linux-x86_64
Version: 0.3.2
Check: package dependencies
Result: ERROR
Packages required and available but unsuitable versions:
'CodelistGenerator', 'CohortCharacteristics', 'OmopSketch',
'PatientProfiles'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64