* using log directory 'd:/Rcompile/CRANpkg/local/4.3/PatientProfiles.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'PatientProfiles' can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-oldrel-windows-x86_64/PatientProfiles-00install.html' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... 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 ... [9s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [5s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [65s] ERROR Running 'spelling.R' [0s] Running 'testthat.R' [64s] 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 ] â•â• Skipped tests (104) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • 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' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Error ('test-addConceptIntersect.R:243:3'): records out of observation ────── Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector' Backtrace: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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: â–† 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 in 'inst/doc' ... OK * checking re-building of vignette outputs ... [69s] 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 ... [19s] OK * checking HTML version of manual ... [8s] OK * DONE Status: 2 ERRORs, 1 WARNING