* using log directory ‘/srv/hornik/tmp/CRAN_pretest/OmopStudyBuilder.Rcheck’
* using R Under development (unstable) (2026-04-22 r89950)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-04-23 13:16:04 UTC
* checking for file ‘OmopStudyBuilder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmopStudyBuilder’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Folu Akintola <folu.akintola@ndorms.ox.ac.uk>’

New submission

Possibly misspelled words in DESCRIPTION:
  CDM (18:12)
  OMOP (3:47, 17:53)

The Title field should be in title case. Current version is:
  ‘Build reproducible network studies for OMOP common data model databases’
In title case that is:
  ‘Build Reproducible Network Studies for OMOP Common Data Model Databases’
* 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 ‘OmopStudyBuilder’ can be installed ... [2s/2s] 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 ... [3s/3s] 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/137s] ERROR
  Running ‘testthat.R’ [11s/137s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OmopStudyBuilder)
  > 
  > test_check("OmopStudyBuilder")
  Saving _problems/test-initStudy-121.R
  Saving _problems/test-initStudy-122.R
  Saving _problems/test-initStudy-123.R
  Saving _problems/test-initStudy-124.R
  
  
  
  
  The following package(s) were not installed successfully:
  - [progress]: install failed
  - [httr]: install failed
  - [CodelistGenerator]: install failed
  - [CDMConnector]: dependency failed (httr, readr)
  - [CohortCharacteristics]: dependency failed (CDMConnector)
  - [CohortConstructor]: dependency failed (CodelistGenerator)
  - [DrugUtilisation]: dependency failed (CodelistGenerator)
  - [IncidencePrevalence]: dependency failed (CDMConnector)
  - [MeasurementDiagnostics]: dependency failed (CohortCharacteristics, CohortConstructor)
  - [OmopSketch]: dependency failed (CohortConstructor)
  - [PhenotypeR]: dependency failed (CodelistGenerator, CohortCharacteristics, CohortConstructor, DrugUtilisation, IncidencePrevalence, MeasurementDiagnostics, OmopSketch, readr)
  - [readr]: dependency failed (vroom)
  - [vroom]: dependency failed (progress)
  You may need to manually download and install these packages.
  
  
  
  
  
  The following package(s) were not installed successfully:
  - [httr]: install failed
  - [progress]: install failed
  - [CodelistGenerator]: install failed
  - [CDMConnector]: dependency failed (httr, readr)
  - [CohortCharacteristics]: dependency failed (CDMConnector)
  - [CohortConstructor]: dependency failed (CodelistGenerator)
  - [DrugUtilisation]: dependency failed (CodelistGenerator)
  - [IncidencePrevalence]: dependency failed (CDMConnector)
  - [MeasurementDiagnostics]: dependency failed (CohortCharacteristics, CohortConstructor)
  - [OmopSketch]: dependency failed (CohortConstructor)
  - [PhenotypeR]: dependency failed (CodelistGenerator, CohortCharacteristics, CohortConstructor, DrugUtilisation, IncidencePrevalence, MeasurementDiagnostics, OmopSketch, readr)
  - [readr]: dependency failed (vroom)
  - [vroom]: dependency failed (progress)
  You may need to manually download and install these packages.
  
  
  
  
  
  
  
  
  
  [ FAIL 4 | WARN 2 | SKIP 17 | PASS 85 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • Docker not available (2): 'test-dockerWrapper.R:8:3',
    'test-dockerWrapper.R:30:3'
  • Integration test - requires built image (1): 'test-dockerWrapper.R:99:3'
  • Integration test - requires built image and config file (1):
    'test-dockerWrapper.R:107:3'
  • Integration test - requires built image and test script (3):
    'test-dockerWrapper.R:103:3', 'test-dockerWrapper.R:111:3',
    'test-dockerWrapper.R:115:3'
  • Integration test - requires built rstudio image (4):
    'test-dockerWrapper.R:65:3', 'test-dockerWrapper.R:69:3',
    'test-dockerWrapper.R:73:3', 'test-dockerWrapper.R:77:3'
  • Integration test - requires running container (2):
    'test-dockerWrapper.R:85:3', 'test-dockerWrapper.R:89:3'
  • Integration test - requires valid renv project (2):
    'test-dockerWrapper.R:53:3', 'test-dockerWrapper.R:57:3'
  • Manual test - set RUN_MANUAL_TESTS=true to run (requires GITHUB_PAT) (2):
    'test-linkGitHub.R:308:3', 'test-linkGitHub.R:342:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-initStudy.R:121:3'): README.md folder labels do not include trailing slashes ──
  Expected `grepl(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-initStudy.R:122:3'): README.md folder labels do not include trailing slashes ──
  Expected `grepl(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-initStudy.R:123:3'): README.md folder labels do not include trailing slashes ──
  Expected `grepl("\\*\\*\\[studyCode\\]\\(studyCode/\\)\\*\\*", readme_text)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-initStudy.R:124:3'): README.md folder labels do not include trailing slashes ──
  Expected `grepl("\\*\\*\\[studyShiny\\]\\(studyShiny/\\)\\*\\*", readme_text)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 4 | WARN 2 | SKIP 17 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s/3s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE