• using R Under development (unstable) (2025-12-05 r89107)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-9) 15.2.0     GNU Fortran (Debian 15.2.0-9) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘PatientProfiles/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PatientProfiles’ version ‘1.4.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... WARNING Cannot process vignettes Packages suggested but not available for checking:   'covr', 'DT', 'gt', 'Hmisc', 'knitr', 'rmarkdown', 'spelling' VignetteBuilder package required for checking but not installed: ‘knitr’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘PatientProfiles’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [10s/14s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [252s/151s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [251s/150s] 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/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(PatientProfiles)   >   > test_check("PatientProfiles")   Starting 2 test processes.   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-addConceptIntersect.R: ! The following columns will be overwritten:   > test-addConceptIntersect.R: * intersect   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * s: count, percentage   > test-summariseResult.R: * v_1: min, q25, median, q75, max   > test-summariseResult.R: * v_2: count, percentage   > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * v_4: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:52.697463   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:52.943347   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * s: count, percentage   > test-summariseResult.R: * v_1: min, q25, median, q75, max   > test-summariseResult.R: * v_2: count, percentage   > test-summariseResult.R: *   > test-summariseResult.R: v_3: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * v_4: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:53.738188   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:54.216968   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * s: count, percentage   > test-summariseResult.R: * v_1: min, q25, median, q75, max   > test-summariseResult.R: * v_2: count, percentage   > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * v_4: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:54.9844   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:55.497245   > test-summariseResult.R: ! names of strata will be ignored   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * s: count, percentage   > test-summariseResult.R: * v_1: min, q25, median, q75, max   > test-summariseResult.R: * v_2: count, percentage   > test-summariseResult.R: * v_3: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * v_4: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:56.348228   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:57.044397   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * cohort_start_date: min, q25, median, q75, max   > test-summariseResult.R: * cohort_end_date: min, q25, median, q75, max   > test-summariseResult.R: * acetaminophen_m365_to_0: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * ibuprophen_m365_to_0: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * naloxone_m365_to_0: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * headache_minf_to_0: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: * covid_minf_to_0: min, q25, median, q75, max, count, percentage   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:05:58.171679   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:05:58.376344   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max   > test-summariseResult.R: * age: min, q25, median, q75, max   > test-summariseResult.R: * age_group: count, percentage   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: * prior_observation: min, q25, median, q75, max   > test-summariseResult.R: * future_observation: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:08.173465   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:08.588949   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max   > test-summariseResult.R: * age: min, q25, median, q75, max   > test-summariseResult.R: * age_group: count, percentage   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: * prior_observation: min, q25, median, q75, max   > test-summariseResult.R: * future_observation: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:09.917808   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:10.360952   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max   > test-summariseResult.R: * age: min, q25, median, q75, max   > test-summariseResult.R: * age_group: count, percentage   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: * prior_observation: min, q25, median, q75, max   > test-summariseResult.R: * future_observation: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:11.770981   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:12.012252   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:12.552131   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:12.758888   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, median, q75, max   > test-summariseResult.R: * age: min, q25, median, q75, max   > test-summariseResult.R: * age_group: count, percentage   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: * prior_observation: min, q25, median, q75, max   > test-summariseResult.R: * future_observation: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:22.508871   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:22.958998   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * condition_start_date: min, q25, median, q75, max   > test-summariseResult.R: * condition_end_date: min, q25, m   > test-summariseResult.R: edian, q75, max   > test-summariseResult.R: * age: min, q25, median, q75, max   > test-summariseResult.R: * age_group: count, percentage   > test-summariseResult.R: * sex: count, percentage   > test-summariseResult.R: * prior_observation: min, q25, median, q75, max   > test-summariseResult.R: * future_observation: min, q25, median, q75, max   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:24.515288   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:24.948116   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:25.579398   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:25.689426   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * group: count   > test-summariseResult.R: * age1: density, mean   > test-summariseResult.R: * age2: density, mean   > test-summariseResult.R: * asthma: density, mean, count   > test-summariseResult.R: * birth: density, mean   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:31.787613   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:32.040127   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * group: count   > test-summariseResult.R: * age1: density, mean   > test-summariseResult.R: * age2: density, mean   > test-summariseResult.R: * asthma: density, mean, count   > test-summariseResult.R: * birth: density, mean   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:32.853218   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:33.408595   > test-summariseResult.R: i The following estimates will be computed:   > test-summariseResult.R: * age1: density   > test-summariseResult.R: ! Table is collected to memory as not all requested estimates are supported on the database side   > test-summariseResult.R: > Start summary of data, at 2025-12-06 13:06:34.173415   > test-summariseResult.R: v Summary finished, at 2025-12-06 13:06:34.321866   Saving _problems/test-summariseResult-59.R   Saving _problems/test-summariseResult-60.R   Saving _problems/test-summariseResult-827.R   Saving _problems/test-summariseResult-831.R   [ FAIL 4 | WARN 53 | SKIP 108 | PASS 176 ]      ══ Skipped tests (108) ═════════════════════════════════════════════════════════   • On CRAN (108): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3',     'test-addCategories.R:70:3', 'test-addCategories.R:109:3',     'test-addCategories.R:157:3', 'test-addConceptIntersect.R:2:3',     'test-addConceptIntersect.R:100:3', 'test-addConceptIntersect.R:152:3',     'test-addConceptIntersect.R:195:3', 'test-addConceptIntersect.R:228:3',     'test-addConceptIntersect.R:261:3', 'test-addCohortIntersect.R:272:3',     'test-addCohortIntersect.R:347:3', 'test-addCohortIntersect.R:393:3',     'test-addCohortIntersect.R:502:3', 'test-addCohortIntersect.R:592:3',     'test-addCohortIntersect.R:650:3', 'test-addCohortIntersect.R:722:3',     'test-addCohortIntersect.R:744:3', 'test-addCohortIntersect.R:830:3',     'test-addCohortIntersect.R:884:3', 'test-addCohortIntersect.R:942:3',     'test-addDeath.R:101:3', 'test-addDeath.R:143:3', 'test-addDeath.R:241:3',     'test-addDeath.R:281:3', 'test-addFutureObservation.R:2:3',     'test-addFutureObservation.R:14:3', 'test-addFutureObservation.R:30:3',     'test-addFutureObservation.R:90:3', 'test-addFutureObservation.R:150:3',     'test-addFutureObservation.R:212:3', 'test-addFutureObservation.R:256:3',     'test-addInObservation.R:2:3', 'test-addInObservation.R:18:3',     'test-addInObservation.R:49:3', 'test-addInObservation.R:173:3',     'test-addIntersect.R:2:3', 'test-addIntersect.R:37:3',     'test-addIntersect.R:226:3', 'test-addIntersect.R:277:3',     'test-addIntersect.R:398:3', 'test-addIntersect.R:502:3',     'test-addIntersect.R:558:3', 'test-addIntersect.R:626:3',     'test-addIntersect.R:775:3', 'test-addIntersect.R:855:3',     'test-addIntersect.R:872:3', 'test-addIntersect.R:942:3',     'test-addIntersect.R:1028:3', 'test-addIntersect.R:1209:3',     'test-addIntersect.R:1225:3', 'test-addObservationPeriodId.R:2:3',     'test-addPriorObservation.R:2:3', 'test-addPriorObservation.R:14:3',     'test-addPriorObservation.R:30:3', 'test-addPriorObservation.R:76:3',     'test-addPriorObservation.R:121:3', 'test-addPriorObservation.R:184:3',     'test-addSex.R:2:3', 'test-addSex.R:16:3', 'test-addSex.R:33:3',     'test-addSex.R:76:3', 'test-addTableIntersect.R:31:3',     'test-addTableIntersect.R:216:3', 'test-addTableIntersect.R:324:3',     'test-addTableIntersect.R:460:3', 'test-addTableIntersect.R:591:3',     'test-benchmarkPatientProfiles.R:2:3', 'test-checks.R:2:3',     'test-checks.R:100:3', 'test-checks.R:153:3', 'test-checks.R:170:3',     'test-checks.R:220:3', 'test-checks.R:247:3', 'test-filterCohortId.R:2:3',     'test-addDemographics.R:2:3', 'test-addDemographics.R:26:3',     'test-addDemographics.R:353:3', 'test-addDemographics.R:422:3',     'test-addDemographics.R:697:3', 'test-addDemographics.R:849:3',     'test-addDemographics.R:870:3', 'test-addDemographics.R:982:3',     'test-addDemographics.R:1058:3', 'test-addDemographics.R:1172:3',     'test-addDemographics.R:1238:3', 'test-addDemographics.R:1267:3',     'test-addDemographics.R:1297:3', 'test-addDemographics.R:1316:3',     'test-addDemographics.R:1330:3', 'test-addDemographics.R:1351:3',     'test-addDemographics.R:1381:3', 'test-format.R:2:3', 'test-format.R:89:3',     'test-format.R:100:3', 'test-format.R:110:3', 'test-format.R:139:3',     'test-mockPatientProfiles.R:2:3', 'test-name.R:2:3', 'test-utilities.R:2:3',     'test-summariseResult.R:255:3', 'test-summariseResult.R:300:3',     'test-summariseResult.R:365:3', 'test-summariseResult.R:409:3',     'test-summariseResult.R:431:3', 'test-summariseResult.R:508:3',     'test-summariseResult.R:596:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-summariseResult.R:57:3'): test all functions ─────────────────   Expected `x2 <- summariseResult(table = x, strata = list(), weights = "w")` not to throw any errors.   Actually got a <rlib_error_package_not_found> with message:     The package "Hmisc" is required.   ── Error ('test-summariseResult.R:60:3'): test all functions ───────────────────   Error in `eval(code, test_env)`: object 'x2' not found   Backtrace:       ▆    1. ├─testthat::expect_true(nrow(x1) == nrow(x2)) at test-summariseResult.R:60:3    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. └─base::nrow(x2)   ── Failure ('test-summariseResult.R:827:3'): density works correctly ───────────   Expected `... <- NULL` not to throw any errors.   Actually got a <rlib_error_package_not_found> with message:     The package "Hmisc" is required.   ── Error ('test-summariseResult.R:828:3'): density works correctly ─────────────   Error in `eval(code, test_env)`: object 'sw' not found   Backtrace:       ▆    1. ├─testthat::expect_equal(...) at test-summariseResult.R:828:3    2. │ └─testthat::quasi_label(enquo(expected), expected.label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. ├─dplyr::pull(...)    5. └─dplyr::filter(...)      [ FAIL 4 | WARN 53 | SKIP 108 | PASS 176 ]   Error:   ! Test failures.   Execution halted
• checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file?
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE