- using R Under development (unstable) (2026-02-18 r89435 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.3.0
GNU Fortran (GCC) 14.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
* current time: 2026-02-19 08:54:21 UTC
- checking for file 'PhenotypeR/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'PhenotypeR' version '0.3.2'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'PhenotypeR' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [1s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [5s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [2s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [444s] ERROR
Running 'testthat.R' [443s]
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 2026-02-19 09:55:25.468971
v Summary finished, at 2026-02-19 09:55:25.654325
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:55:26.714525
v Summary finished, at 2026-02-19 09:55:26.909988
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 2026-02-19 09:55:31.75536
v Summary finished, at 2026-02-19 09:55:32.600368
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:55:33.987286
v Summary finished, at 2026-02-19 09:55:34.233809
> 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 2026-02-19 09:55:47.352749
v Summary finished, at 2026-02-19 09:55:47.562464
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:55:48.611562
v Summary finished, at 2026-02-19 09:55:48.770486
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 2026-02-19 09:55:53.516918
v Summary finished, at 2026-02-19 09:55:54.397116
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:55:55.548218
v Summary finished, at 2026-02-19 09:55:55.872122
> 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 2026-02-19 09:57:12.237402
v Summary finished, at 2026-02-19 09:57:12.427815
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:57:13.440451
v Summary finished, at 2026-02-19 09:57:13.593766
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 2026-02-19 09:57:18.239881
v Summary finished, at 2026-02-19 09:57:18.904063
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:57:20.129967
v Summary finished, at 2026-02-19 09:57:20.440538
> 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 2026-02-19 09:57:27.834635
v Summary finished, at 2026-02-19 09:57:28.015696
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:57:29.054012
v Summary finished, at 2026-02-19 09:57:29.22601
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 2026-02-19 09:57:34.056352
v Summary finished, at 2026-02-19 09:57:34.692063
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:57:35.929187
v Summary finished, at 2026-02-19 09:57:36.170787
> 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 2026-02-19 09:57:43.622627
v Summary finished, at 2026-02-19 09:57:43.798916
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:57:44.909729
v Summary finished, at 2026-02-19 09:57:45.086749
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 2026-02-19 09:57:49.685927
v Summary finished, at 2026-02-19 09:57:50.367447
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:57:51.594004
v Summary finished, at 2026-02-19 09:57:51.875558
> 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 2026-02-19 09:57:59.13921
v Summary finished, at 2026-02-19 09:57:59.332908
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:58:00.4574
v Summary finished, at 2026-02-19 09:58:00.618559
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 2026-02-19 09:58:05.470198
v Summary finished, at 2026-02-19 09:58:06.138595
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:58:07.334447
v Summary finished, at 2026-02-19 09:58:07.616305
> 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 2026-02-19 09:58:15.417896
v Summary finished, at 2026-02-19 09:58:15.589152
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:58:16.714903
v Summary finished, at 2026-02-19 09:58:16.874282
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 2026-02-19 09:58:21.707239
v Summary finished, at 2026-02-19 09:58:22.293138
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:58:23.551523
v Summary finished, at 2026-02-19 09:58:23.858907
> 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 2026-02-19 09:58:31.579693
v Summary finished, at 2026-02-19 09:58:31.747073
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:58:32.855749
v Summary finished, at 2026-02-19 09:58:33.041468
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 2026-02-19 09:58:37.851479
v Summary finished, at 2026-02-19 09:58:38.486886
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:58:39.714057
v Summary finished, at 2026-02-19 09:58:39.970189
> 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 2026-02-19 09:58:47.280443
v Summary finished, at 2026-02-19 09:58:47.422438
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:58:48.450143
v Summary finished, at 2026-02-19 09:58:48.611804
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 2026-02-19 09:58:53.307993
v Summary finished, at 2026-02-19 09:58:54.002507
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:58:55.254679
v Summary finished, at 2026-02-19 09:58:55.48687
> 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 2026-02-19 09:59:02.778581
v Summary finished, at 2026-02-19 09:59:02.973869
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:59:04.039193
v Summary finished, at 2026-02-19 09:59:04.250502
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 2026-02-19 09:59:08.803862
v Summary finished, at 2026-02-19 09:59:09.479979
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:59:10.714126
v Summary finished, at 2026-02-19 09:59:11.02851
> 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 2026-02-19 09:59:18.024089
v Summary finished, at 2026-02-19 09:59:18.193328
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:59:19.215072
v Summary finished, at 2026-02-19 09:59:19.404548
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 2026-02-19 09:59:23.886592
v Summary finished, at 2026-02-19 09:59:24.711936
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:59:25.99338
v Summary finished, at 2026-02-19 09:59:26.305542
> 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 2026-02-19 09:59:33.825352
v Summary finished, at 2026-02-19 09:59:34.025192
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:59:35.103554
v Summary finished, at 2026-02-19 09:59:35.297645
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 2026-02-19 09:59:40.107941
v Summary finished, at 2026-02-19 09:59:40.85565
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:59:42.050903
v Summary finished, at 2026-02-19 09:59:42.337306
> 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 2026-02-19 09:59:49.818736
v Summary finished, at 2026-02-19 09:59:49.994266
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 09:59:51.067166
v Summary finished, at 2026-02-19 09:59:51.24478
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 2026-02-19 09:59:55.959449
v Summary finished, at 2026-02-19 09:59:56.621935
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 09:59:57.815885
v Summary finished, at 2026-02-19 09:59:58.107332
> 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 2026-02-19 10:00:05.354331
v Summary finished, at 2026-02-19 10:00:05.536325
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:00:06.554155
v Summary finished, at 2026-02-19 10:00:06.714683
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 2026-02-19 10:00:11.337123
v Summary finished, at 2026-02-19 10:00:11.908456
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:00:13.18872
v Summary finished, at 2026-02-19 10:00:13.477154
> 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 2026-02-19 10:00:21.021754
v Summary finished, at 2026-02-19 10:00:21.211575
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:00:22.417689
v Summary finished, at 2026-02-19 10:00:22.621543
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 2026-02-19 10:00:27.276242
v Summary finished, at 2026-02-19 10:00:27.908799
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:00:29.135485
v Summary finished, at 2026-02-19 10:00:29.384073
> 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 2026-02-19 10:00:36.895745
v Summary finished, at 2026-02-19 10:00:37.063806
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:00:38.17816
v Summary finished, at 2026-02-19 10:00:38.363038
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 2026-02-19 10:00:42.92025
v Summary finished, at 2026-02-19 10:00:43.533252
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:00:44.800264
v Summary finished, at 2026-02-19 10:00:45.072054
> 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 2026-02-19 10:00:52.321297
v Summary finished, at 2026-02-19 10:00:52.50635
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:00:53.584691
v Summary finished, at 2026-02-19 10:00:53.784727
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 2026-02-19 10:00:58.348563
v Summary finished, at 2026-02-19 10:00:58.994722
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:01:00.246335
v Summary finished, at 2026-02-19 10:01:00.476838
> 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 2026-02-19 10:01:07.874431
v Summary finished, at 2026-02-19 10:01:08.077922
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:01:09.082504
v Summary finished, at 2026-02-19 10:01:09.257995
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 2026-02-19 10:01:14.203896
v Summary finished, at 2026-02-19 10:01:14.924271
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:01:16.186686
v Summary finished, at 2026-02-19 10:01:16.446351
> 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 2026-02-19 10:01:23.937585
v Summary finished, at 2026-02-19 10:01:24.110171
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:01:25.18183
v Summary finished, at 2026-02-19 10:01:25.351809
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 2026-02-19 10:01:29.896243
v Summary finished, at 2026-02-19 10:01:30.627642
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:01:31.884058
v Summary finished, at 2026-02-19 10:01:32.206032
> 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 2026-02-19 10:01:39.564005
v Summary finished, at 2026-02-19 10:01:39.752829
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:01:40.776185
v Summary finished, at 2026-02-19 10:01:40.931263
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 2026-02-19 10:01:45.798639
v Summary finished, at 2026-02-19 10:01:46.490488
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:01:47.727229
v Summary finished, at 2026-02-19 10:01:47.960259
> 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 2026-02-19 10:01:55.288521
v Summary finished, at 2026-02-19 10:01:55.470649
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:01:56.650772
v Summary finished, at 2026-02-19 10:01:56.839285
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 2026-02-19 10:02:01.546366
v Summary finished, at 2026-02-19 10:02:02.209767
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:02:03.437831
v Summary finished, at 2026-02-19 10:02:03.802568
> 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 2026-02-19 10:02:11.223595
v Summary finished, at 2026-02-19 10:02:11.446383
> Getting measurements per subject.
i The following estimates will be calculated:
* measurements_per_subject: min, q25, median, q75, max, density
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2026-02-19 10:02:12.485508
v Summary finished, at 2026-02-19 10:02:12.650836
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 2026-02-19 10:02:17.230305
v Summary finished, at 2026-02-19 10:02:17.947572
> Summarising results - value as concept.
Summarising value as number
i The following estimates will be calculated:
* value_as_concept_id: count, percentage
> Start summary of data, at 2026-02-19 10:02:19.152881
v Summary finished, at 2026-02-19 10:02:19.434069
> 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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [380s] OK
- checking PDF version of manual ... [20s] OK
- checking HTML version of manual ... [5s] OK
- DONE
Status: 1 ERROR