• using R Under development (unstable) (2025-02-21 r87787)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘PatientProfiles/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PatientProfiles’ version ‘1.2.3’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for 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 ... [12s/31s] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... NOTE   Missing dependency on R >= 4.1.0 because package code uses the pipe   |> or function shorthand \(...) syntax added in R 4.1.0.   File(s) using such syntax:     ‘addCategories.R’ ‘addCohortIntersect.R’ ‘addConceptIntersect.R’     ‘addDeath.R’ ‘addDemographics.R’ ‘addDemographicsQuery.R’     ‘addIntersect.R’ ‘addObservationPeriodId.R’ ‘addTableIntersect.R’     ‘checks.R’ ‘formats.R’ ‘mockPatientProfiles.R’ ‘summariseResult.R’     ‘utilities.R’
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... WARNING Missing or unexported object: ‘CDMConnector::cdm_from_con’
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [19s/37s] OK
• checking Rd files ... 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [119s/215s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [118s/213s] 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   [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ]      ══ Skipped tests (104) ═════════════════════════════════════════════════════════   • On CRAN (104): 'test-addAttributes.R:2:3', 'test-addCategories.R:2:3',     'test-addCategories.R:69:3', 'test-addCategories.R:106:3',     'test-addCategories.R:155:3', 'test-addConceptIntersect.R:2:3',     'test-addConceptIntersect.R:97:3', 'test-addConceptIntersect.R:138:3',     'test-addConceptIntersect.R:168:3', 'test-addConceptIntersect.R:199:3',     'test-addDeath.R:104:3', 'test-addDeath.R:149:3', 'test-addDeath.R:247:3',     'test-addDeath.R:290:3', 'test-addCohortIntersect.R:277:3',     'test-addCohortIntersect.R:353:3', 'test-addCohortIntersect.R:398:3',     'test-addCohortIntersect.R:509:3', 'test-addCohortIntersect.R:600:3',     'test-addCohortIntersect.R:660:3', 'test-addCohortIntersect.R:734:3',     'test-addCohortIntersect.R:752:3', 'test-addCohortIntersect.R:838:3',     'test-addFutureObservation.R:2:3', 'test-addFutureObservation.R:13:3',     'test-addFutureObservation.R:27:3', 'test-addFutureObservation.R:87:3',     'test-addFutureObservation.R:147:3', 'test-addFutureObservation.R:209:3',     'test-addFutureObservation.R:253:3', 'test-addInObservation.R:2:3',     'test-addInObservation.R:16:3', 'test-addInObservation.R:47:3',     'test-addInObservation.R:170:3', '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:856:3', 'test-addIntersect.R:870:3',     'test-addIntersect.R:940:3', 'test-addIntersect.R:1027:3',     'test-addIntersect.R:1208:3', 'test-addIntersect.R:1219:3',     'test-addObservationPeriodId.R:2:3', 'test-addPriorObservation.R:2:3',     'test-addPriorObservation.R:13:3', 'test-addPriorObservation.R:27:3',     'test-addPriorObservation.R:73:3', 'test-addPriorObservation.R:118:3',     'test-addPriorObservation.R:180:3', 'test-addSex.R:2:3',     'test-addSex.R:13:3', 'test-addSex.R:25:3', 'test-addSex.R:66:3',     'test-addTableIntersect.R:28:3', 'test-addTableIntersect.R:209:3',     'test-addTableIntersect.R:316:3', 'test-addTableIntersect.R:451:3',     'test-addTableIntersect.R:581:3', 'test-checks.R:2:3', 'test-checks.R:106:3',     'test-checks.R:157:3', 'test-checks.R:177:3', 'test-checks.R:189:3',     'test-checks.R:237:3', 'test-checks.R:264:3', '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-addDemographics.R:2:3', 'test-addDemographics.R:24:3',     'test-addDemographics.R:352:3', 'test-addDemographics.R:419:3',     'test-addDemographics.R:685:3', 'test-addDemographics.R:834:3',     'test-addDemographics.R:852:3', 'test-addDemographics.R:964:3',     'test-addDemographics.R:1043:3', 'test-addDemographics.R:1155:3',     'test-addDemographics.R:1220:3', 'test-addDemographics.R:1246:3',     'test-addDemographics.R:1273:3', 'test-addDemographics.R:1289:3',     'test-addDemographics.R:1300:3', 'test-addDemographics.R:1318:3',     'test-addDemographics.R:1346:3', 'test-utilities.R:2:3',     'test-summariseResult.R:205:3', 'test-summariseResult.R:251:3',     'test-summariseResult.R:308:3', 'test-summariseResult.R:352:3',     'test-summariseResult.R:373:3', 'test-summariseResult.R:448:3',     'test-summariseResult.R:534:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ──────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addConceptIntersect.R:243:3   ── Error ('test-addDeath.R:2:3'): addDeathDate ─────────────────────────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDeath.R:2:3   ── Error ('test-addCohortIntersect.R:6:3'): output format - one outcome cohort ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:6:3   ── Error ('test-addCohortIntersect.R:97:3'): first vs last event - cohort table ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:97:3   ── Error ('test-addCohortIntersect.R:212:3'): multiple cohort entries per person ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addCohortIntersect.R:212:3   ── Error ('test-addInObservation.R:60:3'): addInObservation, window ────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addInObservation.R:60:3   ── Error ('test-addObservationPeriodId.R:193:3'): check when there is the same record in multiple cohorts ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addObservationPeriodId.R:193:3   ── Error ('test-addTableIntersect.R:2:3'): basic structures ────────────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addTableIntersect.R:2:3   ── Error ('test-addTableIntersect.R:162:3'): addTableIntersectCount example ────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addTableIntersect.R:162:3   ── Error ('test-class.R:19:3'): test class consistency across cohort operations ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-class.R:19:3   ── Error ('test-addDemographics.R:45:3'): addDemographics, cohort and condition_occurrence ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:45:3   ── Error ('test-addDemographics.R:84:3'): addDemographics, parameters ──────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:84:3   ── Error ('test-addDemographics.R:149:3'): partial demographics - cohorts ──────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:149:3   ── Error ('test-addDemographics.R:252:3'): partial demographics - omop tables ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:252:3   ── Error ('test-addDemographics.R:324:3'): priorObservation and future_observation - outside of observation period ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:324:3   ── Error ('test-addDemographics.R:540:3'): age at cohort end, no missing, check age computation ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:540:3   ── Error ('test-addDemographics.R:602:3'): age at cohort entry, missing year/month/day of birth ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:602:3   ── Error ('test-addDemographics.R:655:3'): multiple cohortIds, check age at cohort end ──   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-addDemographics.R:655:3   ── Error ('test-addDemographics.R:1365:3'): test query functions ───────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(con = connection(), writeSchema = writeSchema()) at test-addDemographics.R:1365:3   ── Error ('test-summariseResult.R:87:3'): groups and strata ────────────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:87:3   ── Error ('test-summariseResult.R:166:3'): table in db or local ────────────────   Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'   Backtrace:       ▆    1. └─PatientProfiles::mockPatientProfiles(...) at test-summariseResult.R:166:3      [ FAIL 21 | WARN 0 | SKIP 104 | PASS 27 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [125s/329s] ERROR Error(s) in re-building vignettes: --- re-building ‘cohort-intersect.Rmd’ using rmarkdown Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd) Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘cohort-intersect.Rmd’ --- re-building ‘concept-intersect.Rmd’ using rmarkdown Quitting from lines 36-40 [unnamed-chunk-2] (concept-intersect.Rmd) Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘concept-intersect.Rmd’ --- re-building ‘demographics.rmd’ using rmarkdown Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd) Error: processing vignette 'demographics.rmd' failed with diagnostics: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' --- failed re-building ‘demographics.rmd’ --- re-building ‘summarise.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd) Error: processing vignette 'summarise.Rmd' failed with diagnostics: error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': could not find function "eunomia_dir" --- failed re-building ‘summarise.Rmd’ --- re-building ‘table-intersect.Rmd’ using rmarkdown Quitting from lines 35-39 [unnamed-chunk-3] (table-intersect.Rmd) Error: processing vignette 'table-intersect.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘table-intersect.Rmd’ SUMMARY: processing the following files failed:   ‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’   ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [9s/22s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE