Last updated on 2026-02-18 12:52:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.2 | 6.38 | 970.36 | 976.74 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.2 | 3.29 | 668.85 | 672.14 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.2 | 10.00 | 1790.47 | 1800.47 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.2 | 11.00 | 1883.63 | 1894.63 | ERROR | |
| r-devel-macos-arm64 | 0.3.2 | 1.00 | 876.00 | 877.00 | OK | |
| r-devel-windows-x86_64 | 0.3.2 | 8.00 | 732.00 | 740.00 | OK | |
| r-patched-linux-x86_64 | 0.3.2 | 5.48 | 925.82 | 931.30 | OK | |
| r-release-linux-x86_64 | 0.3.2 | 5.93 | 934.10 | 940.03 | OK | |
| r-release-macos-arm64 | 0.3.2 | 1.00 | 1337.00 | 1338.00 | OK | |
| r-release-macos-x86_64 | 0.3.2 | 5.00 | 1798.00 | 1803.00 | OK | |
| r-release-windows-x86_64 | 0.3.2 | 8.00 | 738.00 | 746.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.2 | 1.00 | 1233.00 | 1234.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.2 | 21.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.3.2 | 11.00 | 1064.00 | 1075.00 | OK |
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [16m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PhenotypeR)
>
> test_check("PhenotypeR")
Creating a new cdm
Uploading table person (100 rows) - [1/13]
Uploading table observation_period (100 rows) - [2/13]
Uploading table cdm_source (1 rows) - [3/13]
Uploading table concept (3361 rows) - [4/13]
Uploading table vocabulary (65 rows) - [5/13]
Uploading table concept_relationship (117257 rows) - [6/13]
Uploading table concept_synonym (3895 rows) - [7/13]
Uploading table concept_ancestor (1327 rows) - [8/13]
Uploading table drug_strength (45 rows) - [9/13]
Uploading table condition_occurrence (600 rows) - [10/13]
Uploading table drug_exposure (3100 rows) - [11/13]
Uploading table measurement (2000 rows) - [12/13]
Uploading table my_cohort_1 (100 rows) - [13/13]
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_cohort created.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:19.942469
v Summary finished, at 2026-02-17 19:02:20.346082
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:22.467873
v Summary finished, at 2026-02-17 19:02:22.780007
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:02:32.85104
v Summary finished, at 2026-02-17 19:02:34.366208
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:02:36.67675
v Summary finished, at 2026-02-17 19:02:37.188311
> Binding all diagnostic results.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:05.852675
v Summary finished, at 2026-02-17 19:03:06.255503
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:08.52041
v Summary finished, at 2026-02-17 19:03:08.901068
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:03:19.548274
v Summary finished, at 2026-02-17 19:03:21.149424
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:03:23.39001
v Summary finished, at 2026-02-17 19:03:23.986214
> Binding all diagnostic results.
Saving _problems/test-codelistDiagnostics-129.R
Getting counts of all_measurements codes for cohort all_measurements
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_2 created.
Getting counts of all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
Getting counts of all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_isoenzymes_measurement codes for cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
Getting counts of all_measurements_cyclohexanone_mass_volume_in_urine codes for cohort all_measurements_cyclohexanone_mass_volume_in_urine
Getting counts of all_measurements_phen_x_caffeine_protocol_050301 codes for cohort all_measurements_phen_x_caffeine_protocol_050301
Getting counts of all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
Getting counts of all_measurements_uroporphyrin_iii_measurement codes for cohort all_measurements_uroporphyrin_iii_measurement
Getting counts of all_measurements_uroporphyrin_measurement codes for cohort all_measurements_uroporphyrin_measurement
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:09.855579
v Summary finished, at 2026-02-17 19:06:10.23554
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:12.396744
v Summary finished, at 2026-02-17 19:06:12.75309
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:22.853294
v Summary finished, at 2026-02-17 19:06:24.332938
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:06:27.104036
v Summary finished, at 2026-02-17 19:06:27.680571
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:44.111566
v Summary finished, at 2026-02-17 19:06:44.478918
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:47.048378
v Summary finished, at 2026-02-17 19:06:47.451078
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:06:57.581633
v Summary finished, at 2026-02-17 19:06:59.03098
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:07:01.791752
v Summary finished, at 2026-02-17 19:07:02.371296
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:18.794696
v Summary finished, at 2026-02-17 19:07:19.179173
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:21.469312
v Summary finished, at 2026-02-17 19:07:21.847782
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:31.931729
v Summary finished, at 2026-02-17 19:07:33.374434
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:07:36.09904
v Summary finished, at 2026-02-17 19:07:36.689416
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:53.075769
v Summary finished, at 2026-02-17 19:07:53.491114
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:07:55.969667
v Summary finished, at 2026-02-17 19:07:56.358041
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:06.533499
v Summary finished, at 2026-02-17 19:08:07.930937
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:08:10.534674
v Summary finished, at 2026-02-17 19:08:11.102276
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:27.214442
v Summary finished, at 2026-02-17 19:08:27.599191
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:29.923114
v Summary finished, at 2026-02-17 19:08:30.32219
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:08:40.651071
v Summary finished, at 2026-02-17 19:08:42.064928
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:08:44.716289
v Summary finished, at 2026-02-17 19:08:45.357677
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:01.439668
v Summary finished, at 2026-02-17 19:09:01.820312
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:04.098371
v Summary finished, at 2026-02-17 19:09:04.49205
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:14.601315
v Summary finished, at 2026-02-17 19:09:16.053646
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:09:18.736596
v Summary finished, at 2026-02-17 19:09:19.321692
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:35.149185
v Summary finished, at 2026-02-17 19:09:35.528074
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:37.803187
v Summary finished, at 2026-02-17 19:09:38.182914
i summarising data
i summarising cohort all_measurements_cyclohexanone_mass_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:09:48.162293
v Summary finished, at 2026-02-17 19:09:49.644999
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:09:52.396948
v Summary finished, at 2026-02-17 19:09:53.006458
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:09.044479
v Summary finished, at 2026-02-17 19:10:09.407788
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:11.553768
v Summary finished, at 2026-02-17 19:10:11.953022
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:21.772659
v Summary finished, at 2026-02-17 19:10:23.119711
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:10:25.783937
v Summary finished, at 2026-02-17 19:10:26.404861
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:43.326963
v Summary finished, at 2026-02-17 19:10:43.7327
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:46.300207
v Summary finished, at 2026-02-17 19:10:46.784465
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:10:57.928625
v Summary finished, at 2026-02-17 19:10:59.409077
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:11:01.81373
v Summary finished, at 2026-02-17 19:11:02.316741
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:18.906212
v Summary finished, at 2026-02-17 19:11:19.312222
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:21.717668
v Summary finished, at 2026-02-17 19:11:22.078714
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:32.688206
v Summary finished, at 2026-02-17 19:11:34.308868
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:11:36.843373
v Summary finished, at 2026-02-17 19:11:37.38442
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:52.951859
v Summary finished, at 2026-02-17 19:11:53.341972
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:11:55.424893
v Summary finished, at 2026-02-17 19:11:55.767065
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:06.37646
v Summary finished, at 2026-02-17 19:12:07.900781
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:12:10.80207
v Summary finished, at 2026-02-17 19:12:11.433356
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:28.140717
v Summary finished, at 2026-02-17 19:12:28.508874
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:30.607131
v Summary finished, at 2026-02-17 19:12:30.984202
i summarising data
i summarising cohort all_measurements_uroporphyrin_iii_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:12:42.017257
v Summary finished, at 2026-02-17 19:12:43.438358
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:12:45.952357
v Summary finished, at 2026-02-17 19:12:46.513977
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:02.267266
v Summary finished, at 2026-02-17 19:13:02.690405
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:05.004121
v Summary finished, at 2026-02-17 19:13:05.386207
i summarising data
i summarising cohort all_measurements_uroporphyrin_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:15.54259
v Summary finished, at 2026-02-17 19:13:16.998252
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:13:19.614658
v Summary finished, at 2026-02-17 19:13:20.44168
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:35.701588
v Summary finished, at 2026-02-17 19:13:36.037037
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:38.147465
v Summary finished, at 2026-02-17 19:13:38.531132
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:13:48.843541
v Summary finished, at 2026-02-17 19:13:50.260955
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:13:52.934119
v Summary finished, at 2026-02-17 19:13:53.503865
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:09.37312
v Summary finished, at 2026-02-17 19:14:09.754551
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:12.103301
v Summary finished, at 2026-02-17 19:14:12.473768
i summarising data
i summarising cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:22.958508
v Summary finished, at 2026-02-17 19:14:24.323382
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:14:26.909133
v Summary finished, at 2026-02-17 19:14:27.481115
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:43.035629
v Summary finished, at 2026-02-17 19:14:43.409458
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:45.60716
v Summary finished, at 2026-02-17 19:14:45.984166
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:14:56.320922
v Summary finished, at 2026-02-17 19:14:57.691372
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:15:00.35865
v Summary finished, at 2026-02-17 19:15:00.944541
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:16.719636
v Summary finished, at 2026-02-17 19:15:17.137758
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:19.553144
v Summary finished, at 2026-02-17 19:15:19.941284
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:30.221976
v Summary finished, at 2026-02-17 19:15:31.681422
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:15:34.402144
v Summary finished, at 2026-02-17 19:15:34.989128
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:50.991675
v Summary finished, at 2026-02-17 19:15:51.372625
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:15:53.685364
v Summary finished, at 2026-02-17 19:15:54.084388
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:04.526136
v Summary finished, at 2026-02-17 19:16:05.94065
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:16:08.593709
v Summary finished, at 2026-02-17 19:16:09.188031
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:25.527392
v Summary finished, at 2026-02-17 19:16:25.934673
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:28.190488
v Summary finished, at 2026-02-17 19:16:28.575094
i summarising data
i summarising cohort all_measurements_phen_x_caffeine_protocol_050301
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:38.707321
v Summary finished, at 2026-02-17 19:16:40.139883
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:16:42.813794
v Summary finished, at 2026-02-17 19:16:43.40545
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:16:59.169948
v Summary finished, at 2026-02-17 19:16:59.557532
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:17:01.797891
v Summary finished, at 2026-02-17 19:17:02.166061
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 19:17:12.420436
v Summary finished, at 2026-02-17 19:17:13.802528
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 19:17:16.434776
v Summary finished, at 2026-02-17 19:17:17.035446
> Binding all diagnostic results.
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
══ Skipped tests (23) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-addCodelistAttribute.R:2:3',
'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
'test-drugDiagnostics.R:2:3', 'test-getCohortExpectations.R:3:3',
'test-getCohortExpectations.R:26:3', 'test-getCohortExpectations.R:61:3',
'test-phenotypeDiagnostics.R:3:3', 'test-phenotypeDiagnostics.R:87:3',
'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
'test-shinyDiagnostics.R:46:3'
• empty test (4): 'test-cohortDiagnostics.R:173:1',
'test-cohortDiagnostics.R:177:1', 'test-cohortDiagnostics.R:181:1',
'test-cohortDiagnostics.R:187:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-codelistDiagnostics.R:125:3'): measurementDiagnostics working ──
Expected `... <= 5` to be TRUE.
Differences:
`actual`:
`expected`: TRUE
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17m/48m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PhenotypeR)
>
> test_check("PhenotypeR")
Creating a new cdm
Uploading table person (100 rows) - [1/13]
Uploading table observation_period (100 rows) - [2/13]
Uploading table cdm_source (1 rows) - [3/13]
Uploading table concept (3361 rows) - [4/13]
Uploading table vocabulary (65 rows) - [5/13]
Uploading table concept_relationship (117257 rows) - [6/13]
Uploading table concept_synonym (3895 rows) - [7/13]
Uploading table concept_ancestor (1327 rows) - [8/13]
Uploading table drug_strength (45 rows) - [9/13]
Uploading table condition_occurrence (600 rows) - [10/13]
Uploading table drug_exposure (3100 rows) - [11/13]
Uploading table measurement (2000 rows) - [12/13]
Uploading table my_cohort_1 (100 rows) - [13/13]
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_cohort created.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:19:32.437344
v Summary finished, at 2026-02-17 17:19:33.811444
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:19:43.756279
v Summary finished, at 2026-02-17 17:19:45.040758
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:20:17.717471
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:20:25.46774
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:20:35.929764
v Summary finished, at 2026-02-17 17:20:38.331205
> Binding all diagnostic results.
Getting counts of all_measurements codes for cohort all_measurements
> Getting measurement records based on 20 concepts.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:21:55.632436
v Summary finished, at 2026-02-17 17:21:56.619268
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:22:07.281538
v Summary finished, at 2026-02-17 17:22:08.419101
i summarising data
i summarising cohort all_measurements
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:22:39.303519
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:22:47.780271
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:23:04.028065
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:23:07.247178
> Binding all diagnostic results.
Saving _problems/test-codelistDiagnostics-129.R
Getting counts of all_measurements codes for cohort all_measurements
i Subsetting table measurement using 20 concepts with domain: measurement.
i Combining tables.
i Creating cohort attributes.
i Applying cohort requirements.
i Merging overlapping records.
v Cohort measurement_2 created.
Getting counts of all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum codes for cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
Getting counts of all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma codes for cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
Getting counts of all_measurements_alkaline_phosphatase_isoenzymes_measurement codes for cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
Getting counts of all_measurements_cyclohexanone_mass_volume_in_urine codes for cohort all_measurements_cyclohexanone_mass_volume_in_urine
Getting counts of all_measurements_phen_x_caffeine_protocol_050301 codes for cohort all_measurements_phen_x_caffeine_protocol_050301
Getting counts of all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement codes for cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
Getting counts of all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine codes for cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
Getting counts of all_measurements_uroporphyrin_iii_measurement codes for cohort all_measurements_uroporphyrin_iii_measurement
Getting counts of all_measurements_uroporphyrin_measurement codes for cohort all_measurements_uroporphyrin_measurement
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:32:25.047052
v Summary finished, at 2026-02-17 17:32:26.663556
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:32:37.049485
v Summary finished, at 2026-02-17 17:32:38.986975
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_enzymatic_activity_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:33:25.531442
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:33:32.496655
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:33:42.07422
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:33:44.800601
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:34:27.71252
v Summary finished, at 2026-02-17 17:34:30.021218
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:34:39.939659
v Summary finished, at 2026-02-17 17:34:40.398309
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_alkaline_phosphatase_total_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:35:26.033876
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:35:32.635724
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:35:41.838229
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:35:43.706217
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:36:25.366606
v Summary finished, at 2026-02-17 17:36:26.858542
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:36:35.120296
v Summary finished, at 2026-02-17 17:36:36.423248
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:37:17.089879
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:37:21.8805
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:37:35.106432
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:37:37.554662
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:38:33.580334
v Summary finished, at 2026-02-17 17:38:35.040456
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:38:45.005094
v Summary finished, at 2026-02-17 17:38:46.203275
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:39:15.496118
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:39:20.419325
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:39:31.772235
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:39:34.04124
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:40:30.893179
v Summary finished, at 2026-02-17 17:40:32.818675
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:40:44.941265
v Summary finished, at 2026-02-17 17:40:46.409181
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_mass_volume_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:41:26.97677
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:41:33.644988
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:41:45.438314
v Summary finished, at 2026-02-17 17:41:48.214741
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:42:40.715773
v Summary finished, at 2026-02-17 17:42:42.611387
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:42:51.539685
v Summary finished, at 2026-02-17 17:42:52.81315
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_volume_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:43:30.949866
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:43:38.114868
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:43:51.897787
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:43:54.437541
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:02.088213
v Summary finished, at 2026-02-17 17:45:03.712452
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:11.918732
v Summary finished, at 2026-02-17 17:45:13.540194
i summarising data
i summarising cohort all_measurements_cyclohexanone_mass_volume_in_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:45:53.149677
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:45:59.385087
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:46:14.015355
v Summary finished, at 2026-02-17 17:46:15.48819
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:08.307702
v Summary finished, at 2026-02-17 17:47:08.840982
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:18.514693
v Summary finished, at 2026-02-17 17:47:19.93769
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:47:47.021247
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:47:50.822719
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:47:55.878247
v Summary finished, at 2026-02-17 17:47:58.30402
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:48:31.424
v Summary finished, at 2026-02-17 17:48:32.080838
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:48:37.221476
v Summary finished, at 2026-02-17 17:48:38.850511
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_presence_in_serum_or_plasma
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:06.241469
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:49:08.717035
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:49:15.166657
v Summary finished, at 2026-02-17 17:49:16.688111
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:48.544702
v Summary finished, at 2026-02-17 17:49:49.547263
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:49:54.85452
v Summary finished, at 2026-02-17 17:49:56.84437
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:50:21.955356
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:50:28.643666
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:50:43.294499
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:50:46.531879
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:51:34.367851
v Summary finished, at 2026-02-17 17:51:34.790582
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:51:41.953669
v Summary finished, at 2026-02-17 17:51:42.303404
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_moles_mass_in_stool
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:09.463512
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:52:11.793239
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:52:15.637428
v Summary finished, at 2026-02-17 17:52:16.685729
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:46.387237
v Summary finished, at 2026-02-17 17:52:47.245592
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:52:53.537087
v Summary finished, at 2026-02-17 17:52:54.543273
i summarising data
i summarising cohort all_measurements_uroporphyrin_iii_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:53:22.511507
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:53:29.584009
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:53:37.034934
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:53:39.622445
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:54:29.401701
v Summary finished, at 2026-02-17 17:54:30.615729
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:54:36.850435
v Summary finished, at 2026-02-17 17:54:38.210499
i summarising data
i summarising cohort all_measurements_uroporphyrin_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:08.64764
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:55:12.706535
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:55:20.563302
v Summary finished, at 2026-02-17 17:55:22.219533
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:44.461745
v Summary finished, at 2026-02-17 17:55:44.932321
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:55:52.541106
v Summary finished, at 2026-02-17 17:55:53.674622
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:56:16.68461
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:56:20.857003
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:56:27.038719
v Summary finished, at 2026-02-17 17:56:28.380227
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:56:57.674801
v Summary finished, at 2026-02-17 17:56:58.848567
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:57:07.525557
v Summary finished, at 2026-02-17 17:57:08.88763
i summarising data
i summarising cohort all_measurements_plasma_alkaline_phosphatase_bone_isoenzyme_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:57:35.943478
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:57:38.336685
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:57:43.349699
v Summary finished, at 2026-02-17 17:57:44.871527
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:10.461081
v Summary finished, at 2026-02-17 17:58:11.169447
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:16.650083
v Summary finished, at 2026-02-17 17:58:17.149279
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_measurement_serum
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:58:38.891564
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:58:44.540419
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 17:58:53.555989
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 17...
==============================> 2/2 group-strata combinations @ 2026-02-17 17...
v Summary finished, at 2026-02-17 17:58:56.237386
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:59:36.158056
v Summary finished, at 2026-02-17 17:59:38.611523
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 17:59:44.021942
v Summary finished, at 2026-02-17 17:59:44.493247
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_isoenzymes_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:07.672033
v Summary finished, at 2026-02-17 18:00:11.511974
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:00:18.194567
v Summary finished, at 2026-02-17 18:00:19.685022
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:52.525363
v Summary finished, at 2026-02-17 18:00:53.247886
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:00:58.903271
v Summary finished, at 2026-02-17 18:00:59.668282
i summarising data
i summarising cohort all_measurements_uroporphyrin_3_isomer_mass_time_in_24_hour_urine
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:20.305136
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:01:23.490053
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:01:28.473849
v Summary finished, at 2026-02-17 18:01:30.245683
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:52.397255
v Summary finished, at 2026-02-17 18:01:53.243902
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:01:57.884329
v Summary finished, at 2026-02-17 18:01:58.951531
i summarising data
i summarising cohort all_measurements_phen_x_caffeine_protocol_050301
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:02:15.228605
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:02:18.447197
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:02:27.244568
v Summary finished, at 2026-02-17 18:02:29.167581
> Binding all diagnostic results.
Returning entry cohort as the size of the cohorts to be sampled is equal or smaller than `n`.
> Getting measurement records based on 1 concept.
> Subsetting records to the subjects and timing of interest.
> Getting time between records per person.
Summarising timings
i The following estimates will be calculated:
* days_between_measurements: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:02:58.998619
v Summary finished, at 2026-02-17 18:03:01.110648
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:03:12.609736
v Summary finished, at 2026-02-17 18:03:13.795691
i summarising data
i summarising cohort all_measurements_alkaline_phosphatase_bone_isoenzyme_activity_measurement
v summariseCharacteristics finished!
`group` is not present in settings.
> Summarising results - value as number.
Summarising value as number
i The following estimates will be calculated:
* value_as_number: min, q01, q05, q25, median, q75, q95, q99, max, count_missing, percentage_missing, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-17 18:03:38.27593
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:03:42.242708
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-17 18:03:49.245941
===============>--------------- 1/2 group-strata combinations @ 2026-02-17 18...
==============================> 2/2 group-strata combinations @ 2026-02-17 18...
v Summary finished, at 2026-02-17 18:03:52.852519
> Binding all diagnostic results.
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
══ Skipped tests (23) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-addCodelistAttribute.R:2:3',
'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
'test-drugDiagnostics.R:2:3', 'test-getCohortExpectations.R:3:3',
'test-getCohortExpectations.R:26:3', 'test-getCohortExpectations.R:61:3',
'test-phenotypeDiagnostics.R:3:3', 'test-phenotypeDiagnostics.R:87:3',
'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
'test-shinyDiagnostics.R:46:3'
• empty test (4): 'test-cohortDiagnostics.R:173:1',
'test-cohortDiagnostics.R:177:1', 'test-cohortDiagnostics.R:181:1',
'test-cohortDiagnostics.R:187:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-codelistDiagnostics.R:125:3'): measurementDiagnostics working ──
Expected `... <= 5` to be TRUE.
Differences:
`actual`:
`expected`: TRUE
[ FAIL 1 | WARN 50 | SKIP 23 | PASS 6 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.3.2
Check: 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