* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/CohortCharacteristics.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 whether package ‘CohortCharacteristics’ can be installed ... [12s/38s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/CohortCharacteristics-00install.html' for details.
* checking installed package size ... INFO
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.9Mb
* 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:
    ‘benchmarkCohortCharacteristics.R’ ‘checks.R’ ‘plot.R’
    ‘plotCharacteristics.Rd’ ‘plotCohortAttrition.R’
    ‘plotCohortAttrition.Rd’ ‘plotCohortCount.Rd’ ‘plotCohortTiming.R’
    ‘plotComparedLargeScaleCharacteristics.R’
    ‘plotLargeScaleCharacteristics.R’ ‘summariseCharacteristics.R’
    ‘summariseCharacteristics.Rd’ ‘summariseCohortAttrition.R’
    ‘summariseCohortAttrition.Rd’ ‘summariseCohortCount.R’
    ‘summariseCohortCount.Rd’ ‘summariseCohortOverlap.R’
    ‘summariseCohortOverlap.Rd’ ‘summariseCohortTiming.R’
    ‘summariseCohortTiming.Rd’ ‘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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [22s/71s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/44s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [13m/11m] ERROR
  Running ‘spelling.R’
  Running ‘testthat.R’ [13m/10m]
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 2 | WARN 4 | SKIP 17 | PASS 208 ]
  
  ══ 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-plotLargeScaleCharacteristics.R:3:3',
    'test-summariseCohortCount.R:2:3',
    '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',
    'test-summariseCharacteristics.R:1159:3',
    'test-summariseCharacteristics.R:1389:3',
    'test-summariseCharacteristics.R:1505:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
  Expected `... <- NULL` to run without any errors.
  i Actually got a <rlang_error> with text:
    Failed to collect lazy table.
    Caused by error in `dbSendQuery()`:
    ! rapi_prepare: Failed to prepare query SELECT
      strata_id,
      SUM(variable_00047 * ".data".id_xgv) AS counts_variable_00047,
      SUM(variable_00048 * ".data".id_xgv) AS counts_variable_00048,
      SUM(variable_00049 * ".data".id_xgv) AS counts_variable_00049
    FROM (
      SELECT q01.*, 1.0 AS id_xgv
      FROM (
        SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
        FROM og_066_1740783373
        LEFT JOIN test_dus_cohort_set
          ON (og_066_1740783373.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
        INNER JOIN og_076_1740783383
          ON (test_dus_cohort_set.cohort_name = og_076_1740783383.cohort_name)
      ) q01
    ) q01
    GROUP BY strata_id
    Error: Binder Error: Referenced table ".data" not found!
    Candidate tables: "q01"
    
    LINE 3:   SUM(variable_00047 * ".data".id_xgv) AS counts_variable_00047,
                                   ^
  ── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
  any(...) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [275s/370s] OK
* checking PDF version of manual ... [8s/10s] 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: 1 ERROR, 1 NOTE