* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortSurvival.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 ‘CohortSurvival/DESCRIPTION’ ... OK * this is package ‘CohortSurvival’ version ‘0.6.2’ * 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 ‘CohortSurvival’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/CohortSurvival-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: ‘inputValidation.R’ ‘plotSurvival.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/2s] 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/2s] OK * checking loading without being on the library search path ... [1s/2s] 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 ... [11s/14s] OK * checking Rd files ... [0s/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 ... [1s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [391s/330s] ERROR Running ‘testthat.R’ [390s/329s] 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(CohortSurvival) > > test_check("CohortSurvival") Starting 2 test processes [ FAIL 1 | WARN 42 | SKIP 46 | PASS 39 ] â•â• Skipped tests (46) 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 (46): 'test-addCohortSurvival.R:71:3', 'test-addCohortSurvival.R:158:3', 'test-addCohortSurvival.R:271:3', 'test-addCohortSurvival.R:377:3', 'test-addCohortSurvival.R:489:3', 'test-addCohortSurvival.R:575:3', 'test-addCohortSurvival.R:675:3', 'test-addCohortSurvival.R:762:3', 'test-generateDeathCohort.R:2:3', 'test-generateDeathCohort.R:61:3', 'test-generateDeathCohort.R:128:3', 'test-generateDeathCohort.R:194:3', 'test-generateDeathCohort.R:261:3', 'test-generateDeathCohort.R:349:3', 'test-generateDeathCohort.R:449:3', 'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3', 'test-plotSurvival.R:19:3', 'test-plotSurvival.R:37:3', 'test-plotSurvival.R:57:3', 'test-plotSurvival.R:77:3', 'test-plotSurvival.R:98:3', 'test-plotSurvival.R:129:3', 'test-plotSurvival.R:149:3', 'test-plotSurvival.R:172:3', 'test-plotSurvival.R:191:3', 'test-tableSurvival.R:2:3', 'test-tableSurvival.R:88:3', 'test-estimateSurvival.R:87:3', 'test-estimateSurvival.R:126:3', 'test-estimateSurvival.R:176:3', 'test-estimateSurvival.R:342:3', 'test-estimateSurvival.R:556:3', 'test-estimateSurvival.R:707:3', 'test-estimateSurvival.R:1232:3', 'test-estimateSurvival.R:1358:3', 'test-estimateSurvival.R:1380:3', 'test-estimateSurvival.R:1455:3', 'test-estimateSurvival.R:1651:3', 'test-estimateSurvival.R:1775:3', 'test-estimateSurvival.R:1805:3', 'test-estimateSurvival.R:1824:3', 'test-estimateSurvival.R:1860:3', 'test-estimateSurvival.R:1995:3', 'test-estimateSurvival.R:2124:3', 'test-estimateSurvival.R:2234:5' 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-reexports-omopgenerics.R:15:3'): omopgenerics reexports work ─── Error in `tempdir(check)`: NA in coercion to Rboolean Backtrace: â–† 1. └─base::tempdir("result") at test-reexports-omopgenerics.R:15:3 [ FAIL 1 | WARN 42 | SKIP 46 | PASS 39 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [165s/215s] OK * checking PDF version of manual ... [4s/7s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR, 1 NOTE