* using log directory ‘/srv/hornik/tmp/CRAN/TreatmentPatterns.Rcheck’ * using R Under development (unstable) (2024-01-24 r85824) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (3) Debian flang-new version 17.0.6 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘TreatmentPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TreatmentPatterns’ version ‘2.6.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/8s] NOTE Maintainer: ‘Maarten van Kessel ’ Suggests or Enhances not in mainstream repositories: Eunomia, CohortGenerator, CirceR, Capr Availability using Additional_repositories specification: Eunomia yes https://ohdsi.github.io/drat CohortGenerator yes https://ohdsi.github.io/drat CirceR yes https://ohdsi.github.io/drat Capr yes https://ohdsi.github.io/drat * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'Eunomia', 'CohortGenerator', 'CirceR', 'Capr' * 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 ‘TreatmentPatterns’ can be installed ... [7s/7s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [6s/6s] OK * checking Rd files ... [0s/0s] 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 ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [102s/91s] ERROR Running ‘testthat.R’ [102s/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(TreatmentPatterns) > > test_check("TreatmentPatterns") Starting 2 test processes [ FAIL 8 | WARN 0 | SKIP 28 | PASS 83 ] ══ Skipped tests (28) ══════════════════════════════════════════════════════════ • On CRAN (28): 'test-CDMInterfaceDBC.R:8:3', 'test-CDMInterfaceDBC.R:27:3', 'test-CDMInterfaceDBC.R:40:3', 'test-CDMInterfaceDBC.R:67:3', 'test-CDMInterfaceDBC.R:93:3', 'test-CDMInterfaceDBC.R:129:3', 'test-PathwayConstructor.R:5:3', 'test-PathwayConstructor.R:20:3', 'test-PathwayConstructor.R:38:3', 'test-PathwayConstructor.R:59:3', 'test-PathwayConstructor.R:76:3', 'test-executeTreatmentPatterns.R:9:3', 'test-executeTreatmentPatterns.R:47:3', 'test-export.R:30:3', 'test-export.R:77:3', 'test-export.R:126:3', 'test-export.R:169:3', 'test-export.R:210:3', 'test-export.R:283:3', 'test-export.R:328:3', 'test-export.R:374:3', 'test-export.R:415:3', 'test-export.R:454:3', 'test-export.R:526:3', 'test-computePathways.R:8:3', 'test-computePathways.R:116:3', 'test-computePathways.R:132:3', 'test-computePathways.R:185:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-computePathways.R:32:3'): computePathways CDMConnector ───────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:32:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:53:3'): nrow exitCohorts > 0 ───────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:53:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:73:3'): includeTreatments ──────────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:73:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:148:3'): splitEventCohorts ─────────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:148:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:201:3'): eraCollapseSize ───────────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:201:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:232:3'): combinationWindow ─────────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:232:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:246:3'): minPostCombinationDuration ────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:246:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") ── Error ('test-computePathways.R:260:3'): filterTreatments ──────────────────── Error in `CDMConnector::generateCohortSet(cdm = cdm, cohortSet = cohortsSet, name = cohortTableName, computeAttrition = FALSE)`: The package "CirceR" is required. Backtrace: ▆ 1. └─TreatmentPatterns:::generateCohortTableCDMC() at test-computePathways.R:260:3 2. └─CDMConnector::generateCohortSet(...) at tests/testthat/helper-generateCohortTableCDMC.R:21:3 3. └─rlang::check_installed("CirceR") [ FAIL 8 | WARN 0 | SKIP 28 | PASS 83 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs