* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/CohortSymmetry.Rcheck’
* using R Under development (unstable) (2025-02-11 r87713)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-12) 14.2.0
    GNU Fortran (Debian 14.2.0-12) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CohortSymmetry/DESCRIPTION’ ... OK
* this is package ‘CohortSymmetry’ version ‘0.2.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [7s/11s] OK
* 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 ‘CohortSymmetry’ can be installed ... [4s/5s] 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 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 ... [0s/0s] 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/7s] 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [11s/12s] ERROR
  Running ‘testthat.R’ [11s/11s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(CohortSymmetry)
  > 
  > test_check("CohortSymmetry")
  [ FAIL 7 | WARN 0 | SKIP 58 | PASS 0 ]
  
  ══ Skipped tests (58) ══════════════════════════════════════════════════════════
  • On CRAN (56): 'test-attrition.R:2:3', 'test-attrition.R:63:3',
    'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3',
    'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3',
    'test-dbs.R:2:3', 'test-dbs.R:50:3', 'test-eunomia.R:2:3',
    'test-eunomia.R:65:3', 'test-generateSequenceCohortSet.R:3:3',
    'test-generateSequenceCohortSet.R:20:3',
    'test-generateSequenceCohortSet.R:58:3',
    'test-generateSequenceCohortSet.R:97:3',
    'test-generateSequenceCohortSet.R:154:3',
    'test-generateSequenceCohortSet.R:206:3',
    'test-generateSequenceCohortSet.R:260:3',
    'test-generateSequenceCohortSet.R:289:3',
    'test-generateSequenceCohortSet.R:331:3',
    'test-generateSequenceCohortSet.R:357:3',
    'test-generateSequenceCohortSet.R:428:3',
    'test-generateSequenceCohortSet.R:516:3',
    'test-generateSequenceCohortSet.R:664:3',
    'test-generateSequenceCohortSet.R:752:3',
    'test-generateSequenceCohortSet.R:765:3',
    'test-generateSequenceCohortSet.R:777:3',
    'test-generateSequenceCohortSet.R:789:3',
    'test-generateSequenceCohortSet.R:801:3',
    'test-generateSequenceCohortSet.R:819:3',
    'test-generateSequenceCohortSet.R:837:3',
    'test-generateSequenceCohortSet.R:849:3',
    'test-generateSequenceCohortSet.R:860:3',
    'test-generateSequenceCohortSet.R:871:3',
    'test-generateSequenceCohortSet.R:895:3', 'test-plotSequenceRatio.R:2:3',
    'test-plotSequenceRatio.R:42:3', 'test-plotSequenceRatio.R:80:3',
    'test-plotTemporalSymmetry.R:42:3', 'test-plotTemporalSymmetry.R:85:3',
    'test-summariseSequenceRatios.R:203:3',
    'test-summariseSequenceRatios.R:415:3',
    'test-summariseSequenceRatios.R:522:3',
    'test-summariseSequenceRatios.R:604:3',
    'test-summariseSequenceRatios.R:763:3',
    'test-summariseSequenceRatios.R:801:3',
    'test-summariseSequenceRatios.R:839:3',
    'test-summariseSequenceRatios.R:877:3',
    'test-summariseSequenceRatios.R:960:3',
    'test-summariseTemporalSymmetry.R:71:3',
    'test-summariseTemporalSymmetry.R:96:3', 'test-tableSequenceRatios.R:46:3',
    'test-tableSequenceRatios.R:70:3', 'test-tableTemporalSymmetry.R:46:3',
    'test-tableTemporalSymmetry.R:70:3'
  • {gt} is not installed (2): 'test-tableSequenceRatios.R:2:3',
    'test-tableTemporalSymmetry.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-generateSequenceCohortSet.R:36:3'): one ID against one ID, example 1 ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry()`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:36:3
   2.   └─rlang::check_installed("duckdb")
  ── Error ('test-generateSequenceCohortSet.R:78:3'): one ID against one ID, example 3 ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry()`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:78:3
   2.   └─rlang::check_installed("duckdb")
  ── Error ('test-plotTemporalSymmetry.R:17:3'): plot working ────────────────────
  Error in `(function (cond) 
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", 
      call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", 
  "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─DBI::dbConnect(duckdb::duckdb(), ":memory:") at test-plotTemporalSymmetry.R:17:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-summariseSequenceRatios.R:32:3'): summariseSequenceRatios ──────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:32:3
   2.   └─rlang::check_installed("duckdb")
  ── Error ('test-summariseSequenceRatios.R:97:3'): summariseSequenceRatios - testing ratios and CIs, Example 1 ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:97:3
   2.   └─rlang::check_installed("duckdb")
  ── Error ('test-summariseSequenceRatios.R:164:3'): summariseSequenceRatios - testing ratios and CIs, Example 2 ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:164:3
   2.   └─rlang::check_installed("duckdb")
  ── Error ('test-summariseTemporalSymmetry.R:2:3'): test summariseTemporalSymmetry ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `mockCohortSymmetry()`: The package "duckdb" is required.
  Backtrace:
      ▆
   1. └─CohortSymmetry::mockCohortSymmetry() at test-summariseTemporalSymmetry.R:2:3
   2.   └─rlang::check_installed("duckdb")
  
  [ FAIL 7 | WARN 0 | SKIP 58 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [4s/4s] 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