* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck’
* using R Under development (unstable) (2024-11-07 r87302)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-1) 14.2.0
    GNU Fortran (Debian 14.2.0-1) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘OmopSketch/DESCRIPTION’ ... OK
* this is package ‘OmopSketch’ version ‘0.1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/7s] 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 serialization versions ... OK
* checking whether package ‘OmopSketch’ can be installed ... [3s/3s] 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 ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] ERROR
Running examples in ‘OmopSketch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tableOmopSnapshot
> ### Title: Create a visual table from a summarise_omop_snapshot result.
> ### Aliases: tableOmopSnapshot
> 
> ### ** Examples
> 
> cdm <- mockOmopSketch(numberIndividuals = 10)
> 
> result <- summariseOmopSnapshot(cdm)
> 
> result |>
+   tableOmopSnapshot()
! Results have not been suppressed.
Error in loadNamespace(x) : there is no package called ‘gt’
Calls: tableOmopSnapshot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
mockOmopSketch        6.230  0.340   6.615
summariseOmopSnapshot 4.982  0.201   5.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [128s/66s] ERROR
  Running ‘testthat.R’ [128s/66s]
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(OmopSketch)
  > 
  > test_check("OmopSketch")
  Starting 2 test processes
  [ FAIL 6 | WARN 1 | SKIP 20 | PASS 91 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test-plotInObservation.R:2:3', 'test-mockOmopSketch.R:2:3',
    'test-summariseClinicalRecords.R:2:3',
    'test-summariseClinicalRecords.R:81:3',
    'test-summariseClinicalRecords.R:226:3', 'test-summariseInObservation.R:2:3',
    'test-summariseInObservation.R:96:3', 'test-summariseInObservation.R:148:3',
    'test-summariseInObservation.R:186:3', 'test-summariseConceptCounts.R:2:3',
    'test-summariseConceptCounts.R:428:3', 'test-summariseOmopSnapshot.R:2:3',
    'test-summariseOmopSnapshot.R:10:3',
    'test-summarisePopulationCharacteristics.R:2:3',
    'test-summarisePopulationCharacteristics.R:150:3',
    'test-summarisePopulationCharacteristics.R:166:3',
    'test-summariseRecordCount.R:2:3', 'test-summariseRecordCount.R:92:3',
    'test-summariseRecordCount.R:112:3', 'test-summariseRecordCount.R:191:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-summariseOmopSnapshot.R:28:3'): works with mockOmopSketch ────
  Expected `x <- tableOmopSnapshot(summariseOmopSnapshot(cdm))` to run without any errors.
  i Actually got a <packageNotFoundError> with text:
    there is no package called 'gt'
  ── Error ('test-summariseOmopSnapshot.R:29:3'): works with mockOmopSketch ──────
  Error in `eval(code, test_env)`: object 'x' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(inherits(x, "gt_tbl")) at test-summariseOmopSnapshot.R:29:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::inherits(x, "gt_tbl")
  ── Failure ('test-summariseObservationPeriod.R:164:3'): check summariseObservationPeriod works ──
  Expected `tableObservationPeriod(resAll)` to run without any errors.
  i Actually got a <packageNotFoundError> with text:
    there is no package called 'gt'
  ── Failure ('test-summariseObservationPeriod.R:165:3'): check summariseObservationPeriod works ──
  Expected `tableObservationPeriod(resOne)` to run without any errors.
  i Actually got a <packageNotFoundError> with text:
    there is no package called 'gt'
  ── Failure ('test-summariseObservationPeriod.R:166:3'): check summariseObservationPeriod works ──
  Expected `tableObservationPeriod(resEmpty)` to run without any errors.
  i Actually got a <packageNotFoundError> with text:
    there is no package called 'gt'
  ── Failure ('test-summariseObservationPeriod.R:323:3'): check it works with mockOmopSketch ──
  Expected `tableObservationPeriod(sop)` to run without any errors.
  i Actually got a <packageNotFoundError> with text:
    there is no package called 'gt'
  
  [ FAIL 6 | WARN 1 | SKIP 20 | PASS 91 ]
  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: 2 ERRORs