* using log directory 'd:/Rcompile/CRANpkg/local/4.3/CohortCharacteristics.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 'CohortCharacteristics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CohortCharacteristics' version '0.2.0'
* 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 'CohortCharacteristics' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s] 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 ... WARNING
Codoc mismatches from documentation object 'mockCohortCharacteristics':
mockCohortCharacteristics
  Code: function(con = NULL, writeSchema = NULL, numberIndividuals =
                 10, ..., seed = NULL)
  Docs: function(connectionDetails = list(con =
                 DBI::dbConnect(duckdb::duckdb(), ":memory:"),
                 write_schema = "main", mock_prefix = NULL),
                 drug_exposure = NULL, drug_strength = NULL,
                 observation_period = NULL, condition_occurrence =
                 NULL, visit_occurrence = NULL, concept_ancestor =
                 NULL, person = NULL, death = NULL, cohort1 = NULL,
                 cohort2 = NULL, drug_concept_id_size = 5,
                 ancestor_concept_id_size = 5,
                 condition_concept_id_size = 5, visit_concept_id_size =
                 5, visit_occurrence_id_size = 5,
                 ingredient_concept_id_size = 1, drug_exposure_size =
                 10, patient_size = 1, min_drug_exposure_start_date =
                 "2000-01-01", max_drug_exposure_start_date =
                 "2020-01-01", earliest_date_of_birth = NULL,
                 latest_date_of_birth = NULL,
                 earliest_observation_start_date = NULL,
                 latest_observation_start_date = NULL,
                 min_days_to_observation_end = NULL,
                 max_days_to_observation_end = NULL,
                 earliest_condition_start_date = NULL,
                 latest_condition_start_date = NULL,
                 min_days_to_condition_end = NULL,
                 max_days_to_condition_end = NULL,
                 earliest_visit_start_date = NULL,
                 latest_visit_start_date = NULL, min_days_to_visit_end
                 = NULL, max_days_to_visit_end = NULL, seed = 1, ...)
  Argument names in code not in docs:
    con writeSchema numberIndividuals
  Argument names in docs not in code:
    connectionDetails drug_exposure drug_strength observation_period
    condition_occurrence visit_occurrence concept_ancestor person death
    cohort1 cohort2 drug_concept_id_size ancestor_concept_id_size
    condition_concept_id_size visit_concept_id_size
    visit_occurrence_id_size ingredient_concept_id_size
    drug_exposure_size patient_size min_drug_exposure_start_date
    max_drug_exposure_start_date earliest_date_of_birth
    latest_date_of_birth earliest_observation_start_date
    latest_observation_start_date min_days_to_observation_end
    max_days_to_observation_end earliest_condition_start_date
    latest_condition_start_date min_days_to_condition_end
    max_days_to_condition_end earliest_visit_start_date
    latest_visit_start_date min_days_to_visit_end max_days_to_visit_end
  Mismatches in argument names (first 3):
    Position: 1 Code: con Docs: connectionDetails
    Position: 2 Code: writeSchema Docs: drug_exposure
    Position: 3 Code: numberIndividuals Docs: drug_strength
  Mismatches in argument default values:
    Name: 'seed' Code: NULL Docs: 1

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [3s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [83s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [82s]
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(CohortCharacteristics)
  > 
  > test_check("CohortCharacteristics")
  Starting 2 test processes
  [ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-plotCharacteristics.R:2:3',
    'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
    'test-plotSummarised.R:91:3', 'test-plotSummarised.R:197:3',
    'test-plotSummarised.R:299:3',
    'test-summariseLargeScaleCharacteristics.R:2:3',
    'test-tableSummarised.R:2:3', 'test-tableSummarised.R:123:3',
    'test-summariseCharacteristics.R:1122:3'
  • empty test (1): 'test-tableSummarised.R:262:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-summariseCharacteristics.R:53:3'): test summariseCharacteristics ──
  Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort, 
      person = person, comorbidities = comorbidities, medication = medication, 
      observation_period = observation_period, cohort1 = emptyCohort, 
      cohort2 = emptyCohort)`: ! `con` must be a DBI connection
  Backtrace:
      ▆
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:53:3
   2.   └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
   3.     └─rlang::abort(...)
  ── Error ('test-summariseCharacteristics.R:378:3'): test empty cohort ──────────
  Error in `mockCohortCharacteristics(connectionDetails = connectionDetails)`: tables must be a list; it can not contain NA; it can not be NULL; it has to be named; elements must have class: data.frame.
  Backtrace:
      ▆
   1. └─PatientProfiles (local) mockCohortCharacteristics(connectionDetails = connectionDetails) at test-summariseCharacteristics.R:378:3
   2.   └─PatientProfiles:::assertList(tables, named = TRUE, class = "data.frame")
   3.     └─cli::cli_abort(errorMessage, call = call)
   4.       └─rlang::abort(...)
  ── Error ('test-summariseCharacteristics.R:484:3'): test cohort id ─────────────
  Error in `mockCohortCharacteristics(connectionDetails, dus_cohort = dus_cohort, 
      person = person, comorbidities = comorbidities, medication = medication, 
      observation_period = observation_period, cohort1 = emptyCohort, 
      cohort2 = emptyCohort)`: ! `con` must be a DBI connection
  Backtrace:
      ▆
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:484:3
   2.   └─cli::cli_abort(c(`!` = "`con` must be a DBI connection"))
   3.     └─rlang::abort(...)
  
  [ FAIL 3 | WARN 0 | SKIP 11 | PASS 82 ]
  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 ... [156s] ERROR
Error(s) in re-building vignettes:
--- re-building 'a05_summariseCohortEntries.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

--- finished re-building 'a05_summariseCohortEntries.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a06_summarisePatientCharacteristics.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 78-86 [unnamed-chunk-5] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'a06_summarisePatientCharacteristics.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a07_summariseLargeScaleCharacteristics.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

--- finished re-building 'a07_summariseLargeScaleCharacteristics.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a08_summariseCohortOverlap.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

--- finished re-building 'a08_summariseCohortOverlap.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a09_summariseCohortTiming.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

--- finished re-building 'a09_summariseCohortTiming.Rmd'

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
  'a06_summarisePatientCharacteristics.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [18s] OK
* checking HTML version of manual ... [5s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE