* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortCharacteristics.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CohortCharacteristics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CohortCharacteristics’ version ‘0.4.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘CohortCharacteristics’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/CohortCharacteristics-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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:
    ‘benchmarkCohortCharacteristics.R’ ‘checks.R’ ‘plot.R’
    ‘plotCohortAttrition.R’ ‘plotCohortTiming.R’
    ‘plotComparedLargeScaleCharacteristics.R’
    ‘plotLargeScaleCharacteristics.R’ ‘summariseCharacteristics.R’
    ‘summariseCohortAttrition.R’ ‘summariseCohortCount.R’
    ‘summariseCohortOverlap.R’ ‘summariseCohortTiming.R’
    ‘summariseLargeScaleCharacteristics.R’ ‘table.R’
    ‘tableCharacteristics.R’ ‘tableCohortAttrition.R’
    ‘tableCohortCount.R’ ‘tableCohortOverlap.R’ ‘tableCohortTiming.R’
    ‘tableLargeScaleCharacteristics.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 ... [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 ... 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 ... [13s/20s] OK
* checking Rd files ... [1s/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/6s] ERROR
Running examples in ‘CohortCharacteristics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ###   plot functions.
> ### Aliases: availablePlotColumns
> 
> ### ** Examples
> 
> {
+ cdm <- mockCohortCharacteristics()
+ 
+ result <- summariseCharacteristics(cdm$cohort1)
+ 
+ availablePlotColumns(result)
+ 
+ mockDisconnect(cdm)
+ }
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [146s/91s] ERROR
  Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [146s/91s]
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 12 | WARN 4 | SKIP 17 | PASS 16 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
    'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
    'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
    'test-plotCohortTiming.R:94:3', 'test-summariseCharacteristics.R:1159:3',
    'test-summariseCharacteristics.R:1389:3',
    'test-summariseCharacteristics.R:1505:3', 'test-summariseCohortCount.R:2:3',
    'test-plotLargeScaleCharacteristics.R:3:3',
    'test-summariseLargeScaleCharacteristics.R:2:3',
    'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
    'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
    'test-tableLargeScaleCharacteristics.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plotCohortAttrition.R:2:3'): plot cohort attrition ─────────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-plotCohortAttrition.R:2:3
  ── Error ('test-summariseCharacteristics.R:55:3'): test summariseCharacteristics ──
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:55:3
  ── Error ('test-summariseCharacteristics.R:407:3'): test empty cohort ──────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:407:3
  ── Error ('test-summariseCharacteristics.R:517:3'): test cohort id ─────────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:517:3
  ── Error ('test-summariseCharacteristics.R:654:3'): arguments tableIntersect ───
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:654:3
  ── Error ('test-summariseCharacteristics.R:987:3'): arguments cohortIntersect ──
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:987:3
  ── Error ('test-summariseCharacteristics.R:1360:3'): empty input cohort contains name issue #170 ──
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1360:3
  ── Error ('test-summariseCharacteristics.R:1452:3'): arrange ageGroup ──────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1452:3
  ── Error ('test-summariseCohortAttrition.R:2:3'): check summariseCohortAttrition is deterministic ──
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-summariseCohortAttrition.R:2:3
  ── Error ('test-summariseCohortOverlap.R:41:3'): summariseCohortOverlap ────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:41:3
  ── Error ('test-summariseCohortOverlap.R:246:3'): test countBy ─────────────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:246:3
  ── Error ('test-summariseCohortTiming.R:35:3'): summariseCohortTiming ──────────
  Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
  Backtrace:
      â–†
   1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortTiming.R:35:3
  
  [ FAIL 12 | WARN 4 | SKIP 17 | PASS 16 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [192s/286s] OK
* checking PDF version of manual ... [5s/7s] OK
* checking HTML version of manual ... [1s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE