Last updated on 2026-02-25 07:51:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.2 | 6.64 | 1165.17 | 1171.81 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 3.83 | 49.39 | 53.22 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.2 | 11.00 | 1855.25 | 1866.25 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.3 | 10.00 | 114.84 | 124.84 | OK | |
| r-devel-macos-arm64 | 0.3.3 | 1.00 | 25.00 | 26.00 | OK | |
| r-devel-windows-x86_64 | 0.3.3 | 8.00 | 91.00 | 99.00 | OK | |
| r-patched-linux-x86_64 | 0.3.2 | ERROR | ||||
| r-release-linux-x86_64 | 0.3.2 | 6.12 | 1102.95 | 1109.07 | ERROR | |
| r-release-macos-arm64 | 0.3.3 | 1.00 | 23.00 | 24.00 | OK | |
| r-release-macos-x86_64 | 0.3.2 | 5.00 | 1798.00 | 1803.00 | OK | |
| r-release-windows-x86_64 | 0.3.3 | 9.00 | 109.00 | 118.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.3 | 1.00 | 29.00 | 30.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.2 | 21.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.3.3 | 9.00 | 104.00 | 113.00 | OK |
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [10m/13m]
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 2026-02-23 19:41:26.030413
v Summary finished, at 2026-02-23 19:41:26.292266
> 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 2026-02-23 19:41:27.783403
v Summary finished, at 2026-02-23 19:41:28.008126
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 2026-02-23 19:41:35.215436
v Summary finished, at 2026-02-23 19:41:36.461469
> 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 2026-02-23 19:41:38.589383
v Summary finished, at 2026-02-23 19:41:38.976004
> 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 2026-02-23 19:41:59.522023
v Summary finished, at 2026-02-23 19:41:59.932363
> 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 2026-02-23 19:42:01.439235
v Summary finished, at 2026-02-23 19:42:01.679716
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 2026-02-23 19:42:09.45296
v Summary finished, at 2026-02-23 19:42:11.046864
> 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 2026-02-23 19:42:13.111596
v Summary finished, at 2026-02-23 19:42:13.613935
> 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 2026-02-23 19:44:27.127206
v Summary finished, at 2026-02-23 19:44:27.416479
> 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 2026-02-23 19:44:29.099813
v Summary finished, at 2026-02-23 19:44:29.341799
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 2026-02-23 19:44:37.616305
v Summary finished, at 2026-02-23 19:44:38.902269
> 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 2026-02-23 19:44:41.000161
v Summary finished, at 2026-02-23 19:44:41.544965
> 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 2026-02-23 19:44:55.1043
v Summary finished, at 2026-02-23 19:44:55.357164
> 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 2026-02-23 19:44:57.201137
v Summary finished, at 2026-02-23 19:44:57.542954
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 2026-02-23 19:45:05.269817
v Summary finished, at 2026-02-23 19:45:06.658731
> 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 2026-02-23 19:45:09.39049
v Summary finished, at 2026-02-23 19:45:10.007366
> 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 2026-02-23 19:45:22.560998
v Summary finished, at 2026-02-23 19:45:22.895317
> 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 2026-02-23 19:45:24.765996
v Summary finished, at 2026-02-23 19:45:25.034506
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 2026-02-23 19:45:32.365048
v Summary finished, at 2026-02-23 19:45:33.810776
> 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 2026-02-23 19:45:35.68846
v Summary finished, at 2026-02-23 19:45:36.118475
> 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 2026-02-23 19:45:48.460625
v Summary finished, at 2026-02-23 19:45:48.691582
> 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 2026-02-23 19:45:50.390438
v Summary finished, at 2026-02-23 19:45:50.807456
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 2026-02-23 19:45:58.480341
v Summary finished, at 2026-02-23 19:45:59.418242
> 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 2026-02-23 19:46:01.265983
v Summary finished, at 2026-02-23 19:46:01.644085
> 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 2026-02-23 19:46:14.807972
v Summary finished, at 2026-02-23 19:46:15.210531
> 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 2026-02-23 19:46:17.173311
v Summary finished, at 2026-02-23 19:46:17.606593
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 2026-02-23 19:46:27.196982
v Summary finished, at 2026-02-23 19:46:28.432184
> 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 2026-02-23 19:46:30.952305
v Summary finished, at 2026-02-23 19:46:31.455499
> 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 2026-02-23 19:46:46.431159
v Summary finished, at 2026-02-23 19:46:46.946503
> 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 2026-02-23 19:46:49.150989
v Summary finished, at 2026-02-23 19:46:49.473153
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 2026-02-23 19:46:58.731523
v Summary finished, at 2026-02-23 19:47:00.109637
> 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 2026-02-23 19:47:02.28588
v Summary finished, at 2026-02-23 19:47:02.695393
> 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 2026-02-23 19:47:18.736906
v Summary finished, at 2026-02-23 19:47:19.011263
> 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 2026-02-23 19:47:21.364586
v Summary finished, at 2026-02-23 19:47:21.820113
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 2026-02-23 19:47:31.858135
v Summary finished, at 2026-02-23 19:47:33.424082
> 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 2026-02-23 19:47:35.685957
v Summary finished, at 2026-02-23 19:47:36.421271
> 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 2026-02-23 19:47:51.209411
v Summary finished, at 2026-02-23 19:47:51.587521
> 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 2026-02-23 19:47:53.466707
v Summary finished, at 2026-02-23 19:47:53.797756
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 2026-02-23 19:48:02.78338
v Summary finished, at 2026-02-23 19:48:03.971439
> 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 2026-02-23 19:48:06.581062
v Summary finished, at 2026-02-23 19:48:07.195245
> 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 2026-02-23 19:48:20.135752
v Summary finished, at 2026-02-23 19:48:20.545434
> 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 2026-02-23 19:48:22.530304
v Summary finished, at 2026-02-23 19:48:22.774595
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 2026-02-23 19:48:30.646518
v Summary finished, at 2026-02-23 19:48:31.816508
> 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 2026-02-23 19:48:33.823532
v Summary finished, at 2026-02-23 19:48:34.266693
> 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 2026-02-23 19:48:47.086952
v Summary finished, at 2026-02-23 19:48:47.333458
> 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 2026-02-23 19:48:48.946414
v Summary finished, at 2026-02-23 19:48:49.352607
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 2026-02-23 19:48:57.567059
v Summary finished, at 2026-02-23 19:48:58.568213
> 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 2026-02-23 19:49:00.424611
v Summary finished, at 2026-02-23 19:49:00.963726
> 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 2026-02-23 19:49:12.780373
v Summary finished, at 2026-02-23 19:49:13.209495
> 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 2026-02-23 19:49:15.024696
v Summary finished, at 2026-02-23 19:49:15.277295
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 2026-02-23 19:49:23.46217
v Summary finished, at 2026-02-23 19:49:24.397838
> 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 2026-02-23 19:49:26.871777
v Summary finished, at 2026-02-23 19:49:27.239939
> 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 2026-02-23 19:49:39.816852
v Summary finished, at 2026-02-23 19:49:40.202294
> 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 2026-02-23 19:49:42.100531
v Summary finished, at 2026-02-23 19:49:42.427154
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 2026-02-23 19:49:50.456277
v Summary finished, at 2026-02-23 19:49:51.372175
> 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 2026-02-23 19:49:54.205722
v Summary finished, at 2026-02-23 19:49:54.705697
> 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 2026-02-23 19:50:06.971045
v Summary finished, at 2026-02-23 19:50:07.212519
> 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 2026-02-23 19:50:09.247838
v Summary finished, at 2026-02-23 19:50:09.658186
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 2026-02-23 19:50:18.817381
v Summary finished, at 2026-02-23 19:50:19.766458
> 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 2026-02-23 19:50:21.565648
v Summary finished, at 2026-02-23 19:50:21.940171
> 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 2026-02-23 19:50:33.864252
v Summary finished, at 2026-02-23 19:50:34.121656
> 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 2026-02-23 19:50:35.807016
v Summary finished, at 2026-02-23 19:50:36.070175
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 2026-02-23 19:50:43.989194
v Summary finished, at 2026-02-23 19:50:45.1411
> 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 2026-02-23 19:50:47.409493
v Summary finished, at 2026-02-23 19:50:47.979949
> 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 2026-02-23 19:51:00.35538
v Summary finished, at 2026-02-23 19:51:00.609586
> 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 2026-02-23 19:51:02.623673
v Summary finished, at 2026-02-23 19:51:02.863613
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 2026-02-23 19:51:10.532246
v Summary finished, at 2026-02-23 19:51:11.57382
> 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 2026-02-23 19:51:13.854277
v Summary finished, at 2026-02-23 19:51:14.409578
> 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 2026-02-23 19:51:28.55172
v Summary finished, at 2026-02-23 19:51:28.802343
> 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 2026-02-23 19:51:30.479669
v Summary finished, at 2026-02-23 19:51:30.831141
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 2026-02-23 19:51:39.885517
v Summary finished, at 2026-02-23 19:51:41.041078
> 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 2026-02-23 19:51:42.853822
v Summary finished, at 2026-02-23 19:51:43.20479
> 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 2026-02-23 19:51:55.986939
v Summary finished, at 2026-02-23 19:51:56.225055
> 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 2026-02-23 19:51:57.966901
v Summary finished, at 2026-02-23 19:51:58.215631
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 2026-02-23 19:52:06.369231
v Summary finished, at 2026-02-23 19:52:07.575866
> 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 2026-02-23 19:52:09.724943
v Summary finished, at 2026-02-23 19:52:10.099781
> 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 2026-02-23 19:52:23.522
v Summary finished, at 2026-02-23 19:52:23.925524
> 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 2026-02-23 19:52:25.521244
v Summary finished, at 2026-02-23 19:52:25.829349
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 2026-02-23 19:52:33.686707
v Summary finished, at 2026-02-23 19:52:35.019903
> 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 2026-02-23 19:52:37.196726
v Summary finished, at 2026-02-23 19:52:37.550294
> 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 2026-02-23 19:52:50.319109
v Summary finished, at 2026-02-23 19:52:50.553011
> 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 2026-02-23 19:52:52.472326
v Summary finished, at 2026-02-23 19:52:52.772408
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 2026-02-23 19:53:01.544346
v Summary finished, at 2026-02-23 19:53:02.783068
> 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 2026-02-23 19:53:04.76811
v Summary finished, at 2026-02-23 19:53:05.142105
> 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 2026-02-23 19:53:18.792352
v Summary finished, at 2026-02-23 19:53:19.044116
> 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 2026-02-23 19:53:20.72331
v Summary finished, at 2026-02-23 19:53:21.026791
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 2026-02-23 19:53:30.00765
v Summary finished, at 2026-02-23 19:53:30.972252
> 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 2026-02-23 19:53:33.252776
v Summary finished, at 2026-02-23 19:53:33.624546
> 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-clang
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17m/39m]
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 2026-02-22 20:09:55.93935
v Summary finished, at 2026-02-22 20:09:56.418576
> 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 2026-02-22 20:09:59.632365
v Summary finished, at 2026-02-22 20:10:00.535281
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 2026-02-22 20:10:20.196309
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:10:26.523696
> 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 2026-02-22 20:10:35.126886
v Summary finished, at 2026-02-22 20:10:36.254635
> 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 2026-02-22 20:11:32.420887
v Summary finished, at 2026-02-22 20:11:33.304596
> 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 2026-02-22 20:11:37.805333
v Summary finished, at 2026-02-22 20:11:38.639668
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 2026-02-22 20:11:58.374758
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:12:02.357629
> 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 2026-02-22 20:12:09.135577
v Summary finished, at 2026-02-22 20:12:10.561875
> 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 2026-02-22 20:17:33.227405
v Summary finished, at 2026-02-22 20:17:33.602005
> 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 2026-02-22 20:17:36.387456
v Summary finished, at 2026-02-22 20:17:37.264247
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 2026-02-22 20:17:54.546373
v Summary finished, at 2026-02-22 20:17:56.144258
> 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 2026-02-22 20:18:01.927906
v Summary finished, at 2026-02-22 20:18:03.386527
> 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 2026-02-22 20:18:30.1038
v Summary finished, at 2026-02-22 20:18:30.716758
> 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 2026-02-22 20:18:35.802842
v Summary finished, at 2026-02-22 20:18:36.80128
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 2026-02-22 20:18:58.122216
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:19:03.155248
> 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 2026-02-22 20:19:08.346333
v Summary finished, at 2026-02-22 20:19:09.37607
> 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 2026-02-22 20:19:38.81532
v Summary finished, at 2026-02-22 20:19:39.251751
> 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 2026-02-22 20:19:43.473889
v Summary finished, at 2026-02-22 20:19:44.559894
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 2026-02-22 20:20:10.421026
v Summary finished, at 2026-02-22 20:20:12.627182
> 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 2026-02-22 20:20:17.299219
v Summary finished, at 2026-02-22 20:20:18.207248
> 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 2026-02-22 20:20:44.320072
v Summary finished, at 2026-02-22 20:20:44.860631
> 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 2026-02-22 20:20:48.148142
v Summary finished, at 2026-02-22 20:20:48.693148
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 2026-02-22 20:21:07.187285
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:21:10.492377
> 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 2026-02-22 20:21:15.668313
v Summary finished, at 2026-02-22 20:21:16.852508
> 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 2026-02-22 20:22:03.053979
v Summary finished, at 2026-02-22 20:22:04.590077
> 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 2026-02-22 20:22:17.567432
v Summary finished, at 2026-02-22 20:22:18.958139
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 2026-02-22 20:23:12.266219
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:23:24.469773
> 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 2026-02-22 20:23:36.99059
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:23:46.250081
> 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 2026-02-22 20:24:54.936392
v Summary finished, at 2026-02-22 20:24:56.001405
> 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 2026-02-22 20:25:02.842921
v Summary finished, at 2026-02-22 20:25:04.552368
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 2026-02-22 20:25:53.696749
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:26:01.477828
> 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 2026-02-22 20:26:22.108603
v Summary finished, at 2026-02-22 20:26:25.053416
> 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 2026-02-22 20:27:23.558303
v Summary finished, at 2026-02-22 20:27:25.753254
> 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 2026-02-22 20:27:36.826266
v Summary finished, at 2026-02-22 20:27:39.063023
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 2026-02-22 20:28:09.594004
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:28:13.582259
> 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 2026-02-22 20:28:21.992777
v Summary finished, at 2026-02-22 20:28:23.89607
> 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 2026-02-22 20:28:58.971908
v Summary finished, at 2026-02-22 20:28:59.913268
> 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 2026-02-22 20:29:03.418563
v Summary finished, at 2026-02-22 20:29:03.867016
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 2026-02-22 20:29:22.176521
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:29:25.396145
> 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 2026-02-22 20:29:31.507996
v Summary finished, at 2026-02-22 20:29:32.317278
> 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 2026-02-22 20:30:00.628492
v Summary finished, at 2026-02-22 20:30:01.052947
> 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 2026-02-22 20:30:05.015666
v Summary finished, at 2026-02-22 20:30:05.754731
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 2026-02-22 20:30:23.199368
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:30:25.951284
> 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 2026-02-22 20:30:39.752405
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:30:42.391226
> 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 2026-02-22 20:31:28.722589
v Summary finished, at 2026-02-22 20:31:29.278729
> 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 2026-02-22 20:31:35.875859
v Summary finished, at 2026-02-22 20:31:37.262019
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 2026-02-22 20:32:02.012084
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:32:04.593426
> 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 2026-02-22 20:32:10.162708
v Summary finished, at 2026-02-22 20:32:11.374526
> 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 2026-02-22 20:32:41.20487
v Summary finished, at 2026-02-22 20:32:41.771569
> 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 2026-02-22 20:32:47.61129
v Summary finished, at 2026-02-22 20:32:48.445243
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 2026-02-22 20:33:09.72364
v Summary finished, at 2026-02-22 20:33:12.247178
> 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 2026-02-22 20:33:17.895625
v Summary finished, at 2026-02-22 20:33:19.413846
> 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 2026-02-22 20:33:45.153552
v Summary finished, at 2026-02-22 20:33:45.917338
> 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 2026-02-22 20:33:53.529685
v Summary finished, at 2026-02-22 20:33:55.179382
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 2026-02-22 20:34:39.010473
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:34:46.281345
> 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 2026-02-22 20:35:02.349466
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:35:05.337195
> 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 2026-02-22 20:36:17.431999
v Summary finished, at 2026-02-22 20:36:19.462922
> 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 2026-02-22 20:36:30.271772
v Summary finished, at 2026-02-22 20:36:31.229373
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 2026-02-22 20:37:34.827213
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:37:43.707215
> 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 2026-02-22 20:37:59.601302
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:38:03.239347
> 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 2026-02-22 20:38:49.905623
v Summary finished, at 2026-02-22 20:38:51.309346
> 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 2026-02-22 20:38:59.879301
v Summary finished, at 2026-02-22 20:39:00.310252
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 2026-02-22 20:39:43.821382
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:39:48.427333
> 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 2026-02-22 20:39:57.866587
v Summary finished, at 2026-02-22 20:39:58.800206
> 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 2026-02-22 20:40:30.46529
v Summary finished, at 2026-02-22 20:40:30.820602
> 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 2026-02-22 20:40:33.057065
v Summary finished, at 2026-02-22 20:40:33.434194
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 2026-02-22 20:40:59.884203
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:41:05.28143
> 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 2026-02-22 20:41:14.650851
v Summary finished, at 2026-02-22 20:41:15.956295
> 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 2026-02-22 20:41:44.356771
v Summary finished, at 2026-02-22 20:41:44.768896
> 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 2026-02-22 20:41:47.355965
v Summary finished, at 2026-02-22 20:41:47.873615
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 2026-02-22 20:41:59.989959
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:42:02.962361
> 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 2026-02-22 20:42:07.320914
v Summary finished, at 2026-02-22 20:42:08.303464
> 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 2026-02-22 20:42:34.570837
v Summary finished, at 2026-02-22 20:42:34.985911
> 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 2026-02-22 20:42:38.142175
v Summary finished, at 2026-02-22 20:42:38.582663
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 2026-02-22 20:43:10.971774
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:43:16.122602
> 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 2026-02-22 20:43:23.734325
v Summary finished, at 2026-02-22 20:43:24.501854
> 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 2026-02-22 20:43:56.535701
v Summary finished, at 2026-02-22 20:43:57.129366
> 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 2026-02-22 20:44:02.258373
v Summary finished, at 2026-02-22 20:44:02.719562
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 2026-02-22 20:44:21.674186
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:44:29.758678
> 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 2026-02-22 20:44:37.623984
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:44:40.052593
> 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 2026-02-22 20:45:18.064717
v Summary finished, at 2026-02-22 20:45:18.421793
> 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 2026-02-22 20:45:21.940181
v Summary finished, at 2026-02-22 20:45:22.414651
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 2026-02-22 20:45:38.456379
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:45:42.397012
> 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 2026-02-22 20:45:51.623073
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:45:53.964956
> 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 2026-02-22 20:46:28.861396
v Summary finished, at 2026-02-22 20:46:29.552458
> 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 2026-02-22 20:46:35.128221
v Summary finished, at 2026-02-22 20:46:36.256138
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 2026-02-22 20:46:59.191469
===============>--------------- 1/2 group-strata combinations @ 2026-02-22 20...
==============================> 2/2 group-strata combinations @ 2026-02-22 20...
v Summary finished, at 2026-02-22 20:47:04.359511
> 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 2026-02-22 20:47:12.228513
v Summary finished, at 2026-02-22 20:47:13.866753
> 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’ [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: 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 2026-02-21 07:29:32.303472
v Summary finished, at 2026-02-21 07:29:32.570116
> 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 2026-02-21 07:29:34.298846
v Summary finished, at 2026-02-21 07:29:34.505766
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 2026-02-21 07:29:43.277928
v Summary finished, at 2026-02-21 07:29:44.810205
> 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 2026-02-21 07:29:48.050987
v Summary finished, at 2026-02-21 07:29:48.737074
> 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 2026-02-21 07:30:11.772729
v Summary finished, at 2026-02-21 07:30:12.023779
> 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 2026-02-21 07:30:13.664422
v Summary finished, at 2026-02-21 07:30:13.918646
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 2026-02-21 07:30:22.755748
v Summary finished, at 2026-02-21 07:30:24.393467
> 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 2026-02-21 07:30:26.439559
v Summary finished, at 2026-02-21 07:30:26.816646
> 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 2026-02-21 07:32:38.999489
v Summary finished, at 2026-02-21 07:32:39.264289
> 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 2026-02-21 07:32:40.991577
v Summary finished, at 2026-02-21 07:32:41.225449
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 2026-02-21 07:32:49.37438
v Summary finished, at 2026-02-21 07:32:50.663357
> 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 2026-02-21 07:32:53.018905
v Summary finished, at 2026-02-21 07:32:53.446997
> 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 2026-02-21 07:33:05.226825
v Summary finished, at 2026-02-21 07:33:05.667545
> 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 2026-02-21 07:33:07.142673
v Summary finished, at 2026-02-21 07:33:07.531491
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 2026-02-21 07:33:14.90399
v Summary finished, at 2026-02-21 07:33:15.798561
> 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 2026-02-21 07:33:17.994342
v Summary finished, at 2026-02-21 07:33:18.379584
> 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 2026-02-21 07:33:30.781958
v Summary finished, at 2026-02-21 07:33:31.14506
> 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 2026-02-21 07:33:32.841896
v Summary finished, at 2026-02-21 07:33:33.153079
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 2026-02-21 07:33:40.419317
v Summary finished, at 2026-02-21 07:33:41.570715
> 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 2026-02-21 07:33:43.648052
v Summary finished, at 2026-02-21 07:33:44.007143
> 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 2026-02-21 07:33:55.945287
v Summary finished, at 2026-02-21 07:33:56.18197
> 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 2026-02-21 07:33:57.656892
v Summary finished, at 2026-02-21 07:33:57.909157
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 2026-02-21 07:34:05.385874
v Summary finished, at 2026-02-21 07:34:06.337633
> 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 2026-02-21 07:34:08.506359
v Summary finished, at 2026-02-21 07:34:09.067635
> 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 2026-02-21 07:34:21.147427
v Summary finished, at 2026-02-21 07:34:21.399086
> 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 2026-02-21 07:34:22.93503
v Summary finished, at 2026-02-21 07:34:23.168928
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 2026-02-21 07:34:30.303704
v Summary finished, at 2026-02-21 07:34:31.421683
> 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 2026-02-21 07:34:33.40345
v Summary finished, at 2026-02-21 07:34:33.979537
> 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 2026-02-21 07:34:46.426745
v Summary finished, at 2026-02-21 07:34:46.694809
> 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 2026-02-21 07:34:48.270103
v Summary finished, at 2026-02-21 07:34:48.671549
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 2026-02-21 07:34:55.752224
v Summary finished, at 2026-02-21 07:34:56.922782
> 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 2026-02-21 07:34:58.937654
v Summary finished, at 2026-02-21 07:34:59.279615
> 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 2026-02-21 07:35:11.511331
v Summary finished, at 2026-02-21 07:35:11.939103
> 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 2026-02-21 07:35:13.528335
v Summary finished, at 2026-02-21 07:35:13.880731
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 2026-02-21 07:35:21.668445
v Summary finished, at 2026-02-21 07:35:23.231717
> 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 2026-02-21 07:35:25.197346
v Summary finished, at 2026-02-21 07:35:25.738632
> 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 2026-02-21 07:35:38.698767
v Summary finished, at 2026-02-21 07:35:38.939983
> 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 2026-02-21 07:35:40.746166
v Summary finished, at 2026-02-21 07:35:41.069231
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 2026-02-21 07:35:50.554696
v Summary finished, at 2026-02-21 07:35:51.749686
> 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 2026-02-21 07:35:53.745727
v Summary finished, at 2026-02-21 07:35:54.240324
> 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 2026-02-21 07:36:06.267153
v Summary finished, at 2026-02-21 07:36:06.668357
> 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 2026-02-21 07:36:08.503733
v Summary finished, at 2026-02-21 07:36:08.923247
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 2026-02-21 07:36:17.088228
v Summary finished, at 2026-02-21 07:36:18.03645
> 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 2026-02-21 07:36:19.818676
v Summary finished, at 2026-02-21 07:36:20.215856
> 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 2026-02-21 07:36:32.244187
v Summary finished, at 2026-02-21 07:36:32.657582
> 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 2026-02-21 07:36:34.700959
v Summary finished, at 2026-02-21 07:36:34.928325
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 2026-02-21 07:36:43.014859
v Summary finished, at 2026-02-21 07:36:44.1805
> 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 2026-02-21 07:36:46.145455
v Summary finished, at 2026-02-21 07:36:46.565488
> 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 2026-02-21 07:36:59.238277
v Summary finished, at 2026-02-21 07:36:59.560325
> 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 2026-02-21 07:37:01.343952
v Summary finished, at 2026-02-21 07:37:01.603646
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 2026-02-21 07:37:08.986356
v Summary finished, at 2026-02-21 07:37:10.082376
> 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 2026-02-21 07:37:12.564065
v Summary finished, at 2026-02-21 07:37:12.976463
> 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 2026-02-21 07:37:25.076148
v Summary finished, at 2026-02-21 07:37:25.338876
> 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 2026-02-21 07:37:26.999863
v Summary finished, at 2026-02-21 07:37:27.243895
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 2026-02-21 07:37:34.58189
v Summary finished, at 2026-02-21 07:37:35.893914
> 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 2026-02-21 07:37:38.15109
v Summary finished, at 2026-02-21 07:37:38.770875
> 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 2026-02-21 07:37:50.460253
v Summary finished, at 2026-02-21 07:37:50.719397
> 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 2026-02-21 07:37:52.761871
v Summary finished, at 2026-02-21 07:37:52.998034
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 2026-02-21 07:38:00.81292
v Summary finished, at 2026-02-21 07:38:01.785311
> 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 2026-02-21 07:38:03.786043
v Summary finished, at 2026-02-21 07:38:04.151775
> 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 2026-02-21 07:38:15.404516
v Summary finished, at 2026-02-21 07:38:15.685352
> 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 2026-02-21 07:38:17.354469
v Summary finished, at 2026-02-21 07:38:17.608946
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 2026-02-21 07:38:25.067518
v Summary finished, at 2026-02-21 07:38:26.641875
> 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 2026-02-21 07:38:28.6324
v Summary finished, at 2026-02-21 07:38:28.967869
> 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 2026-02-21 07:38:40.116562
v Summary finished, at 2026-02-21 07:38:40.356395
> 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 2026-02-21 07:38:41.803736
v Summary finished, at 2026-02-21 07:38:42.08006
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 2026-02-21 07:38:50.222523
v Summary finished, at 2026-02-21 07:38:51.036206
> 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 2026-02-21 07:38:52.646672
v Summary finished, at 2026-02-21 07:38:53.016935
> 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 2026-02-21 07:39:05.470503
v Summary finished, at 2026-02-21 07:39:05.748523
> 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 2026-02-21 07:39:07.619751
v Summary finished, at 2026-02-21 07:39:07.98186
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 2026-02-21 07:39:15.919355
v Summary finished, at 2026-02-21 07:39:16.864042
> 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 2026-02-21 07:39:18.71022
v Summary finished, at 2026-02-21 07:39:19.208081
> 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 2026-02-21 07:39:31.317091
v Summary finished, at 2026-02-21 07:39:31.633921
> 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 2026-02-21 07:39:33.418963
v Summary finished, at 2026-02-21 07:39:33.663347
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 2026-02-21 07:39:41.126332
v Summary finished, at 2026-02-21 07:39:42.025674
> 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 2026-02-21 07:39:44.153633
v Summary finished, at 2026-02-21 07:39:44.676126
> 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 2026-02-21 07:39:57.230446
v Summary finished, at 2026-02-21 07:39:57.545036
> 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 2026-02-21 07:39:59.219163
v Summary finished, at 2026-02-21 07:39:59.450234
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 2026-02-21 07:40:07.547161
v Summary finished, at 2026-02-21 07:40:08.716324
> 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 2026-02-21 07:40:10.575383
v Summary finished, at 2026-02-21 07:40:11.041291
> 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 2026-02-21 07:40:22.762778
v Summary finished, at 2026-02-21 07:40:23.014121
> 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 2026-02-21 07:40:24.61328
v Summary finished, at 2026-02-21 07:40:24.87718
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 2026-02-21 07:40:33.147896
v Summary finished, at 2026-02-21 07:40:34.019562
> 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 2026-02-21 07:40:35.960311
v Summary finished, at 2026-02-21 07:40:36.355379
> 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 2026-02-21 07:40:48.690914
v Summary finished, at 2026-02-21 07:40:49.113902
> 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 2026-02-21 07:40:50.553299
v Summary finished, at 2026-02-21 07:40:50.800519
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 2026-02-21 07:40:58.775886
v Summary finished, at 2026-02-21 07:40:59.891884
> 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 2026-02-21 07:41:01.856981
v Summary finished, at 2026-02-21 07:41:02.323716
> 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-release-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