* 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 ] â•â• Skipped tests (17) 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• • 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' 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-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