Package check result: OK Changes to worse in reverse depends: Package: PhenotypeR [Old version: 0.3.1, New version: 0.3.2] Check: tests New result: ERROR Running ‘testthat.R’ [287s/277s] 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") 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 2026-02-09 10:22:57.654335 v Summary finished, at 2026-02-09 10:22:57.795768 > 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 2026-02-09 10:22:58.465733 v Summary finished, at 2026-02-09 10:22:58.585437 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 2026-02-09 10:23:01.809536 v Summary finished, at 2026-02-09 10:23:02.376396 > 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 2026-02-09 10:23:03.191075 v Summary finished, at 2026-02-09 10:23:03.389205 > 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 2026-02-09 10:23:11.588376 v Summary finished, at 2026-02-09 10:23:11.703134 > 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 2026-02-09 10:23:12.372385 v Summary finished, at 2026-02-09 10:23:12.489977 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 2026-02-09 10:23:15.460264 v Summary finished, at 2026-02-09 10:23:16.004715 > 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 2026-02-09 10:23:16.783937 v Summary finished, at 2026-02-09 10:23:17.070868 > 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 2026-02-09 10:24:04.794641 v Summary finished, at 2026-02-09 10:24:04.914301 > 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 2026-02-09 10:24:05.560175 v Summary finished, at 2026-02-09 10:24:05.674503 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 2026-02-09 10:24:08.59387 v Summary finished, at 2026-02-09 10:24:09.008878 > 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 2026-02-09 10:24:09.796247 v Summary finished, at 2026-02-09 10:24:09.979038 > 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 2026-02-09 10:24:14.487205 v Summary finished, at 2026-02-09 10:24:14.603369 > 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 2026-02-09 10:24:15.254241 v Summary finished, at 2026-02-09 10:24:15.366614 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 2026-02-09 10:24:18.284544 v Summary finished, at 2026-02-09 10:24:18.698934 > 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 2026-02-09 10:24:19.468566 v Summary finished, at 2026-02-09 10:24:19.6401 > 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 2026-02-09 10:24:24.293554 v Summary finished, at 2026-02-09 10:24:24.408105 > 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 2026-02-09 10:24:25.0566 v Summary finished, at 2026-02-09 10:24:25.171562 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 2026-02-09 10:24:28.173238 v Summary finished, at 2026-02-09 10:24:28.61412 > 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 2026-02-09 10:24:29.392709 v Summary finished, at 2026-02-09 10:24:29.561774 > 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 2026-02-09 10:24:34.050745 v Summary finished, at 2026-02-09 10:24:34.167079 > 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 2026-02-09 10:24:34.816113 v Summary finished, at 2026-02-09 10:24:34.929284 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 2026-02-09 10:24:37.877002 v Summary finished, at 2026-02-09 10:24:38.315971 > 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 2026-02-09 10:24:39.088759 v Summary finished, at 2026-02-09 10:24:39.271317 > 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 2026-02-09 10:24:43.782492 v Summary finished, at 2026-02-09 10:24:43.899074 > 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 2026-02-09 10:24:44.552679 v Summary finished, at 2026-02-09 10:24:44.665975 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 2026-02-09 10:24:47.752755 v Summary finished, at 2026-02-09 10:24:48.174221 > 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 2026-02-09 10:24:48.934488 v Summary finished, at 2026-02-09 10:24:49.112107 > 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 2026-02-09 10:24:53.628729 v Summary finished, at 2026-02-09 10:24:53.747742 > 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 2026-02-09 10:24:54.423638 v Summary finished, at 2026-02-09 10:24:54.545698 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 2026-02-09 10:24:57.60656 v Summary finished, at 2026-02-09 10:24:58.045685 > 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 2026-02-09 10:24:58.846875 v Summary finished, at 2026-02-09 10:24:59.024881 > 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 2026-02-09 10:25:03.667252 v Summary finished, at 2026-02-09 10:25:03.784661 > 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 2026-02-09 10:25:04.43566 v Summary finished, at 2026-02-09 10:25:04.555918 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 2026-02-09 10:25:07.498745 v Summary finished, at 2026-02-09 10:25:07.916214 > 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 2026-02-09 10:25:08.858873 v Summary finished, at 2026-02-09 10:25:09.032152 > 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 2026-02-09 10:25:13.469355 v Summary finished, at 2026-02-09 10:25:13.585357 > 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 2026-02-09 10:25:14.236184 v Summary finished, at 2026-02-09 10:25:14.344712 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 2026-02-09 10:25:17.362451 v Summary finished, at 2026-02-09 10:25:17.792063 > 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 2026-02-09 10:25:18.579124 v Summary finished, at 2026-02-09 10:25:18.759498 > 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 2026-02-09 10:25:23.322623 v Summary finished, at 2026-02-09 10:25:23.439378 > 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 2026-02-09 10:25:24.089302 v Summary finished, at 2026-02-09 10:25:24.209069 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 2026-02-09 10:25:27.153079 v Summary finished, at 2026-02-09 10:25:27.576572 > 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 2026-02-09 10:25:28.374804 v Summary finished, at 2026-02-09 10:25:28.555929 > 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 2026-02-09 10:25:33.230924 v Summary finished, at 2026-02-09 10:25:33.348399 > 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 2026-02-09 10:25:34.014003 v Summary finished, at 2026-02-09 10:25:34.130682 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 2026-02-09 10:25:37.088439 v Summary finished, at 2026-02-09 10:25:37.53254 > 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 2026-02-09 10:25:38.315076 v Summary finished, at 2026-02-09 10:25:38.496486 > 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 2026-02-09 10:25:42.969668 v Summary finished, at 2026-02-09 10:25:43.080751 > 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 2026-02-09 10:25:43.73131 v Summary finished, at 2026-02-09 10:25:43.850183 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 2026-02-09 10:25:46.779091 v Summary finished, at 2026-02-09 10:25:47.191089 > 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 2026-02-09 10:25:47.961097 v Summary finished, at 2026-02-09 10:25:48.136064 > 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 2026-02-09 10:25:52.780649 v Summary finished, at 2026-02-09 10:25:52.893074 > 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 2026-02-09 10:25:53.535411 v Summary finished, at 2026-02-09 10:25:53.648427 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 2026-02-09 10:25:56.533262 v Summary finished, at 2026-02-09 10:25:56.939516 > 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 2026-02-09 10:25:57.701431 v Summary finished, at 2026-02-09 10:25:57.870228 > 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 2026-02-09 10:26:02.418621 v Summary finished, at 2026-02-09 10:26:02.537697 > 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 2026-02-09 10:26:03.203167 v Summary finished, at 2026-02-09 10:26:03.315055 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 2026-02-09 10:26:06.314265 v Summary finished, at 2026-02-09 10:26:06.739763 > 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 2026-02-09 10:26:07.512106 v Summary finished, at 2026-02-09 10:26:07.683442 > 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 2026-02-09 10:26:12.2061 v Summary finished, at 2026-02-09 10:26:12.450577 > 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 2026-02-09 10:26:13.106878 v Summary finished, at 2026-02-09 10:26:13.217459 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 2026-02-09 10:26:16.11793 v Summary finished, at 2026-02-09 10:26:16.536409 > 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 2026-02-09 10:26:17.303477 v Summary finished, at 2026-02-09 10:26:17.474731 > 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 2026-02-09 10:26:21.980814 v Summary finished, at 2026-02-09 10:26:22.093596 > 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 2026-02-09 10:26:22.744491 v Summary finished, at 2026-02-09 10:26:22.864192 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 2026-02-09 10:26:25.813212 v Summary finished, at 2026-02-09 10:26:26.235271 > 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 2026-02-09 10:26:27.007991 v Summary finished, at 2026-02-09 10:26:27.177635 > 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 2026-02-09 10:26:31.70357 v Summary finished, at 2026-02-09 10:26:31.819768 > 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 2026-02-09 10:26:32.488667 v Summary finished, at 2026-02-09 10:26:32.599184 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 2026-02-09 10:26:35.668268 v Summary finished, at 2026-02-09 10:26:36.089209 > 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 2026-02-09 10:26:36.86842 v Summary finished, at 2026-02-09 10:26:37.056779 > 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 2026-02-09 10:26:41.544052 v Summary finished, at 2026-02-09 10:26:41.663319 > 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 2026-02-09 10:26:42.413861 v Summary finished, at 2026-02-09 10:26:42.535032 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 2026-02-09 10:26:45.527215 v Summary finished, at 2026-02-09 10:26:45.944508 > 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 2026-02-09 10:26:46.735263 v Summary finished, at 2026-02-09 10:26:46.906771 > 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 2026-02-09 10:26:51.45176 v Summary finished, at 2026-02-09 10:26:51.564543 > 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 2026-02-09 10:26:52.21649 v Summary finished, at 2026-02-09 10:26:52.335382 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 2026-02-09 10:26:55.409446 v Summary finished, at 2026-02-09 10:26:55.837949 > 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 2026-02-09 10:26:56.605984 v Summary finished, at 2026-02-09 10:26:56.775568 > 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 2026-02-09 10:27:01.309822 v Summary finished, at 2026-02-09 10:27:01.418673 > 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 2026-02-09 10:27:02.120884 v Summary finished, at 2026-02-09 10:27:02.233777 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 2026-02-09 10:27:05.303411 v Summary finished, at 2026-02-09 10:27:05.74821 > 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 2026-02-09 10:27:06.564306 v Summary finished, at 2026-02-09 10:27:06.746867 > 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 2026-02-09 10:27:11.311681 v Summary finished, at 2026-02-09 10:27:11.424582 > 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 2026-02-09 10:27:12.088574 v Summary finished, at 2026-02-09 10:27:12.201132 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 2026-02-09 10:27:15.39036 v Summary finished, at 2026-02-09 10:27:15.835686 > 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 2026-02-09 10:27:16.650425 v Summary finished, at 2026-02-09 10:27:16.833726 > 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