Package check result: NOTE Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Nuria Mercade-Besora ’ Found the following (possibly) invalid URLs: URL: https://github.com/OHDSI/MeasurementDiagnostics/actions/workflows/R-CMD-check.yaml From: README.md Status: Error Message: Timeout was reached [github.com]: Connection timed out after 60002 milliseconds URL: https://github.com/ohdsi/MeasurementDiagnostics/issues From: DESCRIPTION man/MeasurementDiagnostics-package.Rd Status: Error Message: Timeout was reached [github.com]: Failed to resolve host 'github.com' with timeout after 60000 ms Changes to worse in reverse depends: Package: PhenotypeR Check: tests New result: ERROR Running ‘testthat.R’ [295s/281s] 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 2026-02-16 18:33:18.017243 v Summary finished, at 2026-02-16 18:33:18.138135 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:33:18.790636 v Summary finished, at 2026-02-16 18:33:18.906367 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 2026-02-16 18:33:21.928373 v Summary finished, at 2026-02-16 18:33:22.457974 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:33:23.241977 v Summary finished, at 2026-02-16 18:33:23.424018 > 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 2026-02-16 18:33:31.571052 v Summary finished, at 2026-02-16 18:33:31.683989 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:33:32.341828 v Summary finished, at 2026-02-16 18:33:32.45894 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 2026-02-16 18:33:35.491224 v Summary finished, at 2026-02-16 18:33:36.038529 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:33:36.846198 v Summary finished, at 2026-02-16 18:33:37.150453 > 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 2026-02-16 18:34:25.274909 v Summary finished, at 2026-02-16 18:34:25.384612 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:34:26.032832 v Summary finished, at 2026-02-16 18:34:26.14952 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 2026-02-16 18:34:29.080869 v Summary finished, at 2026-02-16 18:34:29.501639 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:34:30.257298 v Summary finished, at 2026-02-16 18:34:30.432706 > 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 2026-02-16 18:34:35.065438 v Summary finished, at 2026-02-16 18:34:35.173439 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:34:35.857157 v Summary finished, at 2026-02-16 18:34:35.976161 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 2026-02-16 18:34:38.97357 v Summary finished, at 2026-02-16 18:34:39.387856 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:34:40.150499 v Summary finished, at 2026-02-16 18:34:40.325464 > 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 2026-02-16 18:34:45.103355 v Summary finished, at 2026-02-16 18:34:45.217605 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:34:45.941122 v Summary finished, at 2026-02-16 18:34:46.049726 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 2026-02-16 18:34:49.004521 v Summary finished, at 2026-02-16 18:34:49.405237 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:34:50.177741 v Summary finished, at 2026-02-16 18:34:50.345528 > 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 2026-02-16 18:34:55.095433 v Summary finished, at 2026-02-16 18:34:55.242308 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:34:56.017568 v Summary finished, at 2026-02-16 18:34:56.156368 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 2026-02-16 18:34:59.601787 v Summary finished, at 2026-02-16 18:35:00.085857 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:00.975832 v Summary finished, at 2026-02-16 18:35:01.17279 > 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 2026-02-16 18:35:06.433367 v Summary finished, at 2026-02-16 18:35:06.562548 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:07.28244 v Summary finished, at 2026-02-16 18:35:07.403065 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 2026-02-16 18:35:10.702726 v Summary finished, at 2026-02-16 18:35:11.126489 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:11.918614 v Summary finished, at 2026-02-16 18:35:12.095197 > 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 2026-02-16 18:35:16.806769 v Summary finished, at 2026-02-16 18:35:16.92434 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:17.590794 v Summary finished, at 2026-02-16 18:35:17.703007 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 2026-02-16 18:35:20.731874 v Summary finished, at 2026-02-16 18:35:21.160496 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:21.963927 v Summary finished, at 2026-02-16 18:35:22.149475 > 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 2026-02-16 18:35:26.837522 v Summary finished, at 2026-02-16 18:35:26.950609 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:27.6177 v Summary finished, at 2026-02-16 18:35:27.740558 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 2026-02-16 18:35:30.802413 v Summary finished, at 2026-02-16 18:35:31.392786 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:32.14299 v Summary finished, at 2026-02-16 18:35:32.314273 > 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 2026-02-16 18:35:36.792819 v Summary finished, at 2026-02-16 18:35:36.901845 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:37.547797 v Summary finished, at 2026-02-16 18:35:37.66134 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 2026-02-16 18:35:40.565965 v Summary finished, at 2026-02-16 18:35:40.978118 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:41.729152 v Summary finished, at 2026-02-16 18:35:41.899188 > 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 2026-02-16 18:35:46.420376 v Summary finished, at 2026-02-16 18:35:46.53605 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:47.188621 v Summary finished, at 2026-02-16 18:35:47.300189 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 2026-02-16 18:35:50.247695 v Summary finished, at 2026-02-16 18:35:50.659231 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:35:51.426922 v Summary finished, at 2026-02-16 18:35:51.596809 > 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 2026-02-16 18:35:56.217219 v Summary finished, at 2026-02-16 18:35:56.334211 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:35:56.981594 v Summary finished, at 2026-02-16 18:35:57.0877 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 2026-02-16 18:36:00.004025 v Summary finished, at 2026-02-16 18:36:00.410577 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:01.167594 v Summary finished, at 2026-02-16 18:36:01.353752 > 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 2026-02-16 18:36:05.906705 v Summary finished, at 2026-02-16 18:36:06.023156 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:06.682206 v Summary finished, at 2026-02-16 18:36:06.807766 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 2026-02-16 18:36:09.85199 v Summary finished, at 2026-02-16 18:36:10.265092 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:11.036387 v Summary finished, at 2026-02-16 18:36:11.223626 > 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 2026-02-16 18:36:15.976952 v Summary finished, at 2026-02-16 18:36:16.087493 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:16.739471 v Summary finished, at 2026-02-16 18:36:16.853483 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 2026-02-16 18:36:19.797181 v Summary finished, at 2026-02-16 18:36:20.197549 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:20.967268 v Summary finished, at 2026-02-16 18:36:21.141029 > 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 2026-02-16 18:36:25.672721 v Summary finished, at 2026-02-16 18:36:25.788964 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:26.445904 v Summary finished, at 2026-02-16 18:36:26.561037 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 2026-02-16 18:36:29.53475 v Summary finished, at 2026-02-16 18:36:29.963097 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:30.729486 v Summary finished, at 2026-02-16 18:36:30.908915 > 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 2026-02-16 18:36:35.586236 v Summary finished, at 2026-02-16 18:36:35.701051 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:36.339666 v Summary finished, at 2026-02-16 18:36:36.454068 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 2026-02-16 18:36:39.358342 v Summary finished, at 2026-02-16 18:36:39.771699 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:40.532845 v Summary finished, at 2026-02-16 18:36:40.710598 > 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 2026-02-16 18:36:45.241625 v Summary finished, at 2026-02-16 18:36:45.357013 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:46.01371 v Summary finished, at 2026-02-16 18:36:46.131323 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 2026-02-16 18:36:49.171628 v Summary finished, at 2026-02-16 18:36:49.601418 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:36:50.418121 v Summary finished, at 2026-02-16 18:36:50.595528 > 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 2026-02-16 18:36:55.213504 v Summary finished, at 2026-02-16 18:36:55.329503 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:36:56.124894 v Summary finished, at 2026-02-16 18:36:56.246613 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 2026-02-16 18:36:59.208436 v Summary finished, at 2026-02-16 18:36:59.626447 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:37:00.389737 v Summary finished, at 2026-02-16 18:37:00.557334 > 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 2026-02-16 18:37:05.476757 v Summary finished, at 2026-02-16 18:37:05.633384 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:37:06.461253 v Summary finished, at 2026-02-16 18:37:06.62417 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 2026-02-16 18:37:09.71256 v Summary finished, at 2026-02-16 18:37:10.132425 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:37:10.950102 v Summary finished, at 2026-02-16 18:37:11.119736 > 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 2026-02-16 18:37:15.727593 v Summary finished, at 2026-02-16 18:37:15.843041 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:37:16.513606 v Summary finished, at 2026-02-16 18:37:16.624378 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 2026-02-16 18:37:19.782808 v Summary finished, at 2026-02-16 18:37:20.198169 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:37:20.962089 v Summary finished, at 2026-02-16 18:37:21.131328 > 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 2026-02-16 18:37:25.724371 v Summary finished, at 2026-02-16 18:37:25.833997 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:37:26.494284 v Summary finished, at 2026-02-16 18:37:26.612385 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 2026-02-16 18:37:29.564319 v Summary finished, at 2026-02-16 18:37:29.98377 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:37:30.755881 v Summary finished, at 2026-02-16 18:37:30.927856 > 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 2026-02-16 18:37:35.516919 v Summary finished, at 2026-02-16 18:37:35.625612 > Getting measurements per subject. i The following estimates will be calculated: * measurements_per_subject: min, q25, median, q75, max, density ! Table is collected to memory as not all requested estimates are supported on the database side > Start summary of data, at 2026-02-16 18:37:36.286589 v Summary finished, at 2026-02-16 18:37:36.404279 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 2026-02-16 18:37:39.572996 v Summary finished, at 2026-02-16 18:37:39.989779 > Summarising results - value as concept. Summarising value as number i The following estimates will be calculated: * value_as_concept_id: count, percentage > Start summary of data, at 2026-02-16 18:37:40.756491 v Summary finished, at 2026-02-16 18:37:40.92606 > 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