* using log directory ‘/srv/hornik/tmp/CRAN_pretest/OmopSketch.Rcheck’
* using R Under development (unstable) (2024-09-23 r87189)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘OmopSketch/DESCRIPTION’ ... OK
* this is package ‘OmopSketch’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] NOTE
Maintainer: ‘Marta Alcalde-Herraiz <marta.alcaldeherraiz@ndorms.ox.ac.uk>’

New submission

Possibly misspelled words in DESCRIPTION:
  OMOP (2:34, 28:35)
* 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 ... [0s/0s] 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 ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [5s/5s] 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 ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [51s/30s] ERROR
  Running ‘testthat.R’ [51s/30s]
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 10 | WARN 0 | SKIP 20 | PASS 35 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (20): 'test-mockOmopSketch.R:2:3', 'test-plotInObservation.R:2:3',
    'test-summariseClinicalRecords.R:2:3',
    'test-summariseClinicalRecords.R:81:3',
    'test-summariseClinicalRecords.R:214:3', 'test-summariseInObservation.R:2:3',
    'test-summariseInObservation.R:96:3', 'test-summariseInObservation.R:148:3',
    'test-summariseInObservation.R:184:3', 'test-summariseOmopSnapshot.R:2:3',
    'test-summariseOmopSnapshot.R:10:3', 'test-summariseConceptCounts.R:2:3',
    'test-summariseConceptCounts.R:428:3', 'test-summariseRecordCount.R:2:3',
    'test-summariseRecordCount.R:92:3', 'test-summariseRecordCount.R:112:3',
    'test-summariseRecordCount.R:189:3',
    'test-summarisePopulationCharacteristics.R:2:3',
    'test-summarisePopulationCharacteristics.R:151:3',
    'test-summarisePopulationCharacteristics.R:167:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-summariseObservationPeriod.R:41:3'): check summariseObservationPeriod works ──
  Expected `resAll <- summariseObservationPeriod(cdm$observation_period)` to run without any errors.
  i Actually got a <simpleError> with text:
    unused argument (minFutureObservation = NULL)
  ── Failure ('test-summariseObservationPeriod.R:42:3'): check summariseObservationPeriod works ──
  Expected `... <- NULL` to run without any errors.
  i Actually got a <simpleError> with text:
    unused argument (minFutureObservation = NULL)
  ── Failure ('test-summariseObservationPeriod.R:44:3'): check summariseObservationPeriod works ──
  Expected `... <- NULL` to run without any errors.
  i Actually got a <simpleError> with text:
    unused argument (minFutureObservation = NULL)
  ── Error ('test-summariseObservationPeriod.R:4:5'): check summariseObservationPeriod works ──
  Error in `eval(code, test_env)`: object 'resAllD' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-summariseObservationPeriod.R:49:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─OmopSketch (local) removeSettings(...)
   5. ├─dplyr::mutate(...) at test-summariseObservationPeriod.R:4:5
   6. └─dplyr::filter(resAllD, !is.na(variable_level))
  ── Error ('test-summariseObservationPeriod.R:276:3'): check it works with mockOmopSketch ──
  Error in `CohortConstructor::demographicsCohort(cdm, name = paste0(tablePrefix, 
      "demographics_table"), sex = NULL, ageRange = ageGroup, minPriorObservation = NULL, 
      minFutureObservation = NULL)`: unused argument (minFutureObservation = NULL)
  Backtrace:
       ▆
    1. ├─OmopSketch::summariseObservationPeriod(cdm$observation_period) at test-summariseObservationPeriod.R:276:3
    2. │ ├─dplyr::collect(...)
    3. │ ├─dplyr::select(...)
    4. │ ├─dplyr::ungroup(...)
    5. │ ├─... %>% ...
    6. │ ├─dplyr::mutate(...)
    7. │ ├─dplyr::arrange(...)
    8. │ ├─dplyr::group_by(...)
    9. │ ├─dplyr::select(...)
   10. │ ├─OmopSketch:::filterPersonId(...)
   11. │ │ └─omopgenerics::cdmReference(omopTable)
   12. │ │   └─omopgenerics::assertClass(table, "cdm_table")
   13. │ │     ├─omopgenerics:::checkClass(...)
   14. │ │     ├─omopgenerics:::checkLength(...)
   15. │ │     ├─omopgenerics:::checkNull(createCheckObject(x), null)
   16. │ │     └─omopgenerics:::createCheckObject(x)
   17. │ └─OmopSketch:::addStrataToPeopleInObservation(...)
   18. │   ├─base::suppressWarnings(...)
   19. │   │ └─base::withCallingHandlers(...)
   20. │   └─base::suppressMessages(...)
   21. │     └─base::withCallingHandlers(...)
   22. └─dplyr::mutate(...)
  ── Failure ('test-summariseObservationPeriod.R:372:3'): check summariseObservationPeriod strata works ──
  Expected `... <- NULL` to run without any errors.
  i Actually got a <simpleError> with text:
    unused argument (minFutureObservation = NULL)
  ── Failure ('test-summariseObservationPeriod.R:374:3'): check summariseObservationPeriod strata works ──
  Expected `... <- NULL` to run without any errors.
  i Actually got a <simpleError> with text:
    unused argument (minFutureObservation = NULL)
  ── Error ('test-summariseObservationPeriod.R:379:3'): check summariseObservationPeriod strata works ──
  Error in `eval(code, test_env)`: object 'resStrata' not found
  Backtrace:
      ▆
   1. ├─dplyr::inner_join(...) at test-summariseObservationPeriod.R:379:3
   2. ├─dplyr::rename(...)
   3. └─dplyr::filter(...)
  ── Failure ('test-summarisePopulationCharacteristics.R:127:3'): summarisePopulationCharacteristics() works ──
  `... <- NULL` did not throw the expected warning.
  ── Failure ('test-summarisePopulationCharacteristics.R:185:3'): summarisePopulationCharacteristics() works with mockOmopSKetch ──
  `summarisedPopulation <- summarisePopulationCharacteristics(cdm = cdm)` did not throw the expected warning.
  
  [ FAIL 10 | WARN 0 | SKIP 20 | PASS 35 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [62s/71s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown

Quitting from lines 48-51 [unnamed-chunk-3] (A-summarise_clinical_tables_records.Rmd)
Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `CohortConstructor::demographicsCohort()`:
! unused argument (minFutureObservation = NULL)
--- failed re-building ‘A-summarise_clinical_tables_records.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘B-summarise_concept_counts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

** Processing: /srv/hornik/tmp/CRAN_pretest/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34134 bytes
Input file size = 34260 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 31877
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 31028
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 31028

Output IDAT size = 31028 bytes (3106 bytes decrease)
Output file size = 31106 bytes (3154 bytes = 9.21% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-9-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 34134 bytes
Input file size = 34260 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 31877
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 31028
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 5		IDAT size = 31028

Output IDAT size = 31028 bytes (3106 bytes decrease)
Output file size = 31106 bytes (3154 bytes = 9.21% decrease)

** Processing: /srv/hornik/tmp/CRAN_pretest/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/B-summarise_concept_counts_files/figure-html/unnamed-chunk-10-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 67404 bytes
Input file size = 67578 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 59568
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 59568

Output IDAT size = 59568 bytes (7836 bytes decrease)
Output file size = 59646 bytes (7932 bytes = 11.74% decrease)

--- finished re-building ‘B-summarise_concept_counts.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘C-summarise_pop_characteristics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

--- finished re-building ‘C-summarise_pop_characteristics.Rmd’

Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
  ‘A-summarise_clinical_tables_records.Rmd’

Error: Vignette re-building failed.
Execution halted

* 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, 1 NOTE