* using log directory 'd:/RCompile/CRANincoming/R-devel/FAIRmaterials.Rcheck'
* using R Under development (unstable) (2025-02-18 r87748 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'FAIRmaterials/DESCRIPTION' ... OK
* this is package 'FAIRmaterials' version '0.4.2.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [16s] NOTE
Maintainer: 'Roger H French <roger.french@case.edu>'

This build time stamp is over a month old.
* 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 serialization versions ... OK
* checking whether package 'FAIRmaterials' 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 ... 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 ... 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 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 ... 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(FAIRmaterials)
  > 
  > test_check("FAIRmaterials")
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\PV"
  [1] "Incorrect Unicode property. (U_REGEX_PROPERTY_SYNTAX, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\PV`)"
  Process completed successfully. Outputs saved in the specified folder.
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay`)"
  Process completed successfully. Outputs saved in the specified folder.
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay`)"
  Process completed successfully. Outputs saved in the specified folder.
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\XRay`)"
  Process completed successfully. Outputs saved in the specified folder.
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output`)"
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output/PV"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output`)"
  [1] "D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output/XRay"
  [1] "Back-reference to a non-existent capture group. (U_REGEX_INVALID_BACK_REF, context=`D:\\temp\\2025_02_19_18_50_17_30060\\Rtmp6BgNCg\\output`)"
  Process completed successfully. Outputs saved in the specified folder.
  [ FAIL 17 | WARN 4 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-process_ontology_files.R:22:3'): The output files are correctly generated for PV data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.ttl"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  TTL output file is missing for PV data
  ── Failure ('test-process_ontology_files.R:26:3'): The output files are correctly generated for PV data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.jsonld"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  JSON-LD output file is missing for PV data
  ── Failure ('test-process_ontology_files.R:30:3'): The output files are correctly generated for PV data ──
  file.exists(file.path(output_dir, "rdf_graph_graphviz.svg")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  SVG plot output file is missing for PV data
  ── Failure ('test-process_ontology_files.R:56:3'): The output files are correctly generated for XRay data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.ttl"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  TTL output file is missing for XRay data
  ── Failure ('test-process_ontology_files.R:60:3'): The output files are correctly generated for XRay data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.jsonld"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  JSON-LD output file is missing for XRay data
  ── Failure ('test-process_ontology_files.R:64:3'): The output files are correctly generated for XRay data ──
  file.exists(file.path(output_dir, "rdf_graph_graphviz.svg")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  SVG plot output file is missing for XRay data
  ── Error ('test-process_ontology_files.R:89:3'): Output files are correctly generated and different with external ontology info for XRay data ──
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readLines(...) at test-process_ontology_files.R:89:3
   2.   └─base::file(con, "r")
  ── Error ('test-process_ontology_files.R:138:3'): Output files are correctly generated and different with value type inclusion for XRay data ──
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readLines(file.path(output_dir, "rdf_graph_graphviz.svg")) at test-process_ontology_files.R:138:3
   2.   └─base::file(con, "r")
  ── Failure ('test-process_ontology_files.R:188:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, paste0(sub_dir_foldername, "_ontology_data-output.ttl"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  TTL output file is missing in PV
  ── Failure ('test-process_ontology_files.R:192:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, paste0(sub_dir_foldername, "_ontology_data-output.jsonld"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  JSON-LD output file is missing in PV
  ── Failure ('test-process_ontology_files.R:196:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, "rdf_graph_graphviz.svg")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  SVG plot output file is missing in PV
  ── Failure ('test-process_ontology_files.R:188:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, paste0(sub_dir_foldername, "_ontology_data-output.ttl"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  TTL output file is missing in XRay
  ── Failure ('test-process_ontology_files.R:192:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, paste0(sub_dir_foldername, "_ontology_data-output.jsonld"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  JSON-LD output file is missing in XRay
  ── Failure ('test-process_ontology_files.R:196:5'): The output files are correctly generated for merged data ──
  file.exists(file.path(sub_dir, "rdf_graph_graphviz.svg")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  SVG plot output file is missing in XRay
  ── Failure ('test-process_ontology_files.R:201:3'): The output files are correctly generated for merged data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.ttl"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  TTL output file is missing in data
  ── Failure ('test-process_ontology_files.R:205:3'): The output files are correctly generated for merged data ──
  file.exists(file.path(output_dir, paste0(dir_foldername, "_ontology_data-output.jsonld"))) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  JSON-LD output file is missing in data
  ── Failure ('test-process_ontology_files.R:209:3'): The output files are correctly generated for merged data ──
  file.exists(file.path(output_dir, "rdf_graph_graphviz.svg")) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  SVG plot output file is missing in data
  
  [ FAIL 17 | WARN 4 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE