* using log directory ‘/srv/hornik/tmp/CRAN/FAIRmaterials.Rcheck’
* using R Under development (unstable) (2024-06-20 r86796)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.5 (2)
    Debian flang-new version 18.1.5 (2)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘FAIRmaterials/DESCRIPTION’ ... OK
* this is package ‘FAIRmaterials’ version ‘0.4.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/9s] NOTE
Maintainer: ‘Roger H French <roger.french@case.edu>’

New maintainer:
  Roger H French <roger.french@case.edu>
Old maintainer(s):
  Roger French <roger.french@case.edu>

Possibly misspelled words in DESCRIPTION:
  CSVs (361:75)
  EE (368:52, 368:69)
  EERE (367:55)
  FAIRification (2:33)
  LD (359:73)
  RDF (359:15, 359:34)
  README (362:71)
  SETO (368:26)
  ontologies (365:13, 365:49)
* 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 ‘FAIRmaterials’ 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 ... [1s/1s] 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 ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘FAIRmaterials-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: process_ontology_files
> ### Title: Process Ontology CSV Files
> ### Aliases: process_ontology_files
> 
> ### ** Examples
> 
> # Process the CSV files in the XRay folder
> example_folder1 <- system.file("extdata", "Xray", package = "FAIRmaterials")
> process_ontology_files(example_folder1, add_external_onto_info = FALSE)
Warning in normalizePath(folder_path) :
  path[1]="": No such file or directory
Error in process_files(all_files, main_dir, include_valuetype = include_graph_valuetype,  : 
  Missing required CSV files in the folder.
Calls: process_ontology_files -> process_files
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [8s/7s] ERROR
  Running ‘testthat.R’ [8s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FAIRmaterials)
  > 
  > test_check("FAIRmaterials")
  Process completed successfully. Outputs saved in the specified folder.
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-process_ontology_files.R:28:3'): The output files are correctly generated for Xray data ──
  Error in `process_files(all_files, main_dir, include_valuetype = include_graph_valuetype, 
      update_missing = add_external_onto_info, mergeTitle = merge_title, 
      mergeAuthor = merge_author, mergeVersion = merge_version, 
      mergeURL = merge_base_uri, mergedescription = merge_description)`: Missing required CSV files in the folder.
  Backtrace:
      ▆
   1. └─FAIRmaterials::process_ontology_files(xray_test_folder, add_external_onto_info = FALSE) at test-process_ontology_files.R:28:3
   2.   └─FAIRmaterials:::process_files(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘FAIRmaterials.Rmd’ using rmarkdown
Warning: The 'python' engine in knitr requires the reticulate package. If you do not want to use the reticulate package, set the chunk option python.reticulate = FALSE.

Quitting from lines 92-93 [unnamed-chunk-7] (FAIRmaterials.Rmd)
Error: processing vignette 'FAIRmaterials.Rmd' failed with diagnostics:
there is no package called 'reticulate'
--- failed re-building ‘FAIRmaterials.Rmd’

SUMMARY: processing the following file failed:
  ‘FAIRmaterials.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: 3 ERRORs, 1 NOTE