* using log directory 'd:/RCompile/CRANincoming/R-devel/boilerplate.Rcheck'
* using R Under development (unstable) (2025-06-11 r88304 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'boilerplate/DESCRIPTION' ... OK
* this is package 'boilerplate' version '1.2.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Joseph Bulbulia <joseph.bulbulia@gmail.com>'

New submission
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'boilerplate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'submit_to_cran.R'
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [13s] OK
* checking Rd files ... 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(boilerplate)
  boilerplate 1.2.0
  > 
  > test_check("boilerplate")
  [ FAIL 15 | WARN 1 | SKIP 4 | PASS 527 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-init-functions.R:155:3'
  • Project listing not supported in temp directories with flat structure (1):
    'test-project-functions.R:112:3'
  • Projects in temp directories use flat structure (1):
    'test-project-functions.R:89:3'
  • Special characters test: structure not as expected (1):
    'test-migration-utilities.R:315:9'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-import-export.R:53:3'): boilerplate_import and boilerplate_export work correctly ──
  Error in `boilerplate_export(db = unified_db, data_path = export_dir, output_file = "exported.rds", 
      save_by_category = TRUE, quiet = TRUE, confirm = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\test_import_export2dbac140f1e97/export/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_export(...) at test-import-export.R:53:3
  ── Error ('test-import-export.R:87:3'): boilerplate_export handles selective export ──
  Error in `boilerplate_export(db = test_db, select_elements = "methods.sample", 
      data_path = export_dir, output_file = "boilerplate_export.rds", 
      quiet = TRUE, confirm = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6/selective_export/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_export(...) at test-import-export.R:87:3
  ── Error ('test-import-export.R:121:3'): boilerplate_export handles wildcard selection ──
  Error in `boilerplate_export(db = test_db, select_elements = "methods.statistical.*", 
      data_path = export_dir, output_file = "boilerplate_export.rds", 
      quiet = TRUE, confirm = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6/wildcard_export/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_export(...) at test-import-export.R:121:3
  ── Error ('test-import-export.R:277:3'): boilerplate_export handles complex selection patterns ──
  Error in `boilerplate_export(db = test_db, select_elements = c("methods.statistical.longitudinal.*", 
      "results.main"), data_path = temp_dir, output_file = "multi_select.rds", 
      save_by_category = FALSE, quiet = TRUE, confirm = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\file2dbac2d95ef3/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_export(...) at test-import-export.R:277:3
  ── Error ('test-import-export.R:335:3'): boilerplate_save handles different save modes ──
  Error in `boilerplate_save(db = test_db, data_path = output_dir, category = NULL, 
      confirm = FALSE, quiet = TRUE, timestamp = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\file2dbac3b9118b3/output/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_save(...) at test-import-export.R:335:3
  ── Error ('test-import-export.R:392:3'): import/export functions handle errors gracefully ──
  Error in `boilerplate_import(data_path = empty_data_dir, quiet = TRUE)`: Data path does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\file2dbac6dde5117/empty_data/projects/default/data
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_import(data_path = empty_data_dir, quiet = TRUE) at test-import-export.R:392:3
  ── Error ('test-import-export.R:446:3'): boilerplate_export preserves database structure ──
  Error in `boilerplate_export(db = test_db, data_path = temp_dir, output_file = "preserved.rds", 
      quiet = TRUE, confirm = FALSE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\file2dbac3bce7e4a/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_export(...) at test-import-export.R:446:3
  ── Error ('test-json-support.R:117:3'): boilerplate_import handles JSON files ──
  Error in `boilerplate_import(data_path = test_data_dir, quiet = TRUE)`: Data path does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6/test_json_import/projects/default/data
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_import(data_path = test_data_dir, quiet = TRUE) at test-json-support.R:117:3
  ── Error ('test-json-support.R:161:3'): boilerplate_save handles JSON format ───
  Error in `boilerplate_save(test_db$methods, data_path = test_data_dir, 
      category = "methods", format = "json", confirm = FALSE, quiet = TRUE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6/test_json_save/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_save(...) at test-json-support.R:161:3
  ── Error ('test-json-support.R:373:3'): JSON databases maintain compatibility with RDS workflows ──
  Error in `boilerplate_save(test_db, data_path = test_path, format = "both", 
      confirm = FALSE, quiet = TRUE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6/compat_test/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_save(...) at test-json-support.R:373:3
  ── Failure ('test-project-functions.R:20:3'): project parameter works in core functions ──
  file.exists(file.path(temp_dir, "boilerplate_unified.json")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-project-functions.R:157:3'): boilerplate_copy_from_project works ──
  dest_db$measures$anxiety$description not equal to "Anxiety scale".
  target is NULL, current is character
  ── Failure ('test-project-functions.R:159:3'): boilerplate_copy_from_project works ──
  dest_db$measures$anxiety$items not equal to 10.
  target is NULL, current is numeric
  ── Failure ('test-project-functions.R:221:3'): default project maintains backward compatibility ──
  file.exists(file.path(temp_dir, "boilerplate_unified.json")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error ('test-utilities.R:148:3'): file path utilities work correctly ────────
  Error in `boilerplate_save(db, data_path = temp_dir, confirm = FALSE, quiet = TRUE)`: Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpwPIMz6\file2dbac7d751c41/projects/default/data. Set create_dirs=TRUE to create it.
  Backtrace:
      ▆
   1. └─boilerplate::boilerplate_save(...) at test-utilities.R:148:3
  
  [ FAIL 15 | WARN 1 | SKIP 4 | PASS 527 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s] ERROR
Error(s) in re-building vignettes:
--- re-building 'boilerplate-architecture.Rmd' using rmarkdown
--- finished re-building 'boilerplate-architecture.Rmd'

--- re-building 'boilerplate-bibliography-workflow.Rmd' using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'yaml' (must be registered via knit_engines$set()).
--- finished re-building 'boilerplate-bibliography-workflow.Rmd'

--- re-building 'boilerplate-getting-started.Rmd' using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'markdown' (must be registered via knit_engines$set()).
--- finished re-building 'boilerplate-getting-started.Rmd'

--- re-building 'boilerplate-internals.Rmd' using rmarkdown
--- finished re-building 'boilerplate-internals.Rmd'

--- re-building 'boilerplate-intro-enhanced.Rmd' using rmarkdown
--- finished re-building 'boilerplate-intro-enhanced.Rmd'

--- re-building 'boilerplate-intro.Rmd' using rmarkdown
--- finished re-building 'boilerplate-intro.Rmd'

--- re-building 'boilerplate-json-schema.Rmd' using rmarkdown
--- finished re-building 'boilerplate-json-schema.Rmd'

--- re-building 'boilerplate-json-workflow.Rmd' using rmarkdown

Quitting from boilerplate-json-workflow.Rmd:35-86 [json-basic]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `boilerplate_save()`:
! Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpCqbWfh/json_example/projects/default/data. Set create_dirs=TRUE to create it.
---
Backtrace:
    ▆
 1. └─boilerplate::boilerplate_save(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'boilerplate-json-workflow.Rmd' failed with diagnostics:
Directory does not exist: D:\temp\2025_06_12_16_45_17_25820\RtmpCqbWfh/json_example/projects/default/data. Set create_dirs=TRUE to create it.
--- failed re-building 'boilerplate-json-workflow.Rmd'

--- re-building 'boilerplate-measures-workflow.Rmd' using rmarkdown
--- finished re-building 'boilerplate-measures-workflow.Rmd'

--- re-building 'boilerplate-projects.Rmd' using rmarkdown
--- finished re-building 'boilerplate-projects.Rmd'

--- re-building 'boilerplate-quarto-workflow.Rmd' using rmarkdown
--- finished re-building 'boilerplate-quarto-workflow.Rmd'

--- re-building 'version-management-section.Rmd' using rmarkdown
--- finished re-building 'version-management-section.Rmd'

SUMMARY: processing the following file failed:
  'boilerplate-json-workflow.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs