Last updated on 2026-02-28 11:49:33 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.3 | 6.34 | 69.29 | 75.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 3.67 | 49.29 | 52.96 | 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 | 116.42 | 126.42 | 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 | 90.00 | 98.00 | OK | |
| r-patched-linux-x86_64 | 0.3.3 | 5.27 | 60.74 | 66.01 | OK | |
| 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 | 0.3.3 | 5.00 | 177.00 | 182.00 | 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 | 0.3.3 | 12.00 | 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’ [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 2026-02-21 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: 0.3.3
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.