• 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 ‘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 ... [11s/28s] 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:     ‘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 ... 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 ... [18s/28s] 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 ... ERROR Running examples in ‘CohortCharacteristics-Ex.R’ failed The error most likely occurred in: > ### 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 ... [228s/314s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [227s/313s] 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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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:       ▆    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 ... [5m/12m] OK
• checking PDF version of manual ... [8s/17s] 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