Package: FAIRmaterials
Check: examples
New result: 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
  > 
  > # Create temporary directory
  > temp_dir <- tempdir()
  > XRay_test_folder <- file.path(temp_dir, "XRay")
  > dir.create(XRay_test_folder, recursive = TRUE)
  > 
  > # Copy CSV files from the package's extdata to the temporary directory
  > extdata_path <- system.file("extdata", "XRay", package = "FAIRmaterials")
  > file.copy(from = list.files(extdata_path, full.names = TRUE),
  +   to = XRay_test_folder, recursive = TRUE)
  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
  > 
  > # Process the CSV files in temp the XRay folder
  > process_ontology_files(XRay_test_folder, add_external_onto_info = FALSE)
  Error in get_attr_tbl(line) : object '.' not found
  Calls: process_ontology_files ... <Anonymous> -> list2 -> get_attr_tbl -> gsub -> gsub
  Execution halted

Package: FAIRmaterials
Check: tests
New result: ERROR
    Running ‘testthat.R’ [27s/26s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(FAIRmaterials)
    > 
    > test_check("FAIRmaterials")
    Saving _problems/test-process_ontology_files-17.R
    Saving _problems/test-process_ontology_files-48.R
    Saving _problems/test-process_ontology_files-79.R
    Saving _problems/test-process_ontology_files-124.R
    Saving _problems/test-process_ontology_files-169.R
    [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-process_ontology_files.R:17:3'): The output files are correctly generated for PV data ──
    <objectNotFoundError/error/condition>
    Error in `get_attr_tbl(line)`: object '.' not found
    Backtrace:
         ▆
      1. └─FAIRmaterials::process_ontology_files(PV_test_folder, add_external_onto_info = FALSE) at test-process_ontology_files.R:17:3
      2.   └─FAIRmaterials:::process_files(...)
      3.     └─FAIRmaterials:::plot_ontology_tree2(...)
      4.       └─DiagrammeR::render_graph(...)
      5.         └─DiagrammeR:::get_svg_tbl(svg_vec)
      6.           ├─dplyr::bind_cols(dplyr::tibble(index = i, type = "svg"), get_attr_tbl(line))
      7.           │ └─rlang::list2(...)
      8.           └─DiagrammeR:::get_attr_tbl(line)
      9.             ├─base::gsub(...)
     10.             └─base::gsub(gsub("<[a-z]*? ", "", line), "\"", "'", .)
    ── Error ('test-process_ontology_files.R:48:3'): The output files are correctly generated for XRay data ──
    <objectNotFoundError/error/condition>
    Error in `get_attr_tbl(line)`: object '.' not found
    Backtrace:
         ▆
      1. └─FAIRmaterials::process_ontology_files(XRay_test_folder, add_external_onto_info = FALSE) at test-process_ontology_files.R:48:3
      2.   └─FAIRmaterials:::process_files(...)
      3.     └─FAIRmaterials:::plot_ontology_tree2(...)
      4.       └─DiagrammeR::render_graph(...)
      5.         └─DiagrammeR:::get_svg_tbl(svg_vec)
      6.           ├─dplyr::bind_cols(dplyr::tibble(index = i, type = "svg"), get_attr_tbl(line))
      7.           │ └─rlang::list2(...)
      8.           └─DiagrammeR:::get_attr_tbl(line)
      9.             ├─base::gsub(...)
     10.             └─base::gsub(gsub("<[a-z]*? ", "", line), "\"", "'", .)
    ── Error ('test-process_ontology_files.R:79:3'): Output files are correctly generated and different with external ontology info for XRay data ──
    <objectNotFoundError/error/condition>
    Error in `get_attr_tbl(line)`: object '.' not found
    Backtrace:
         ▆
      1. └─FAIRmaterials::process_ontology_files(XRay_test_folder, add_external_onto_info = FALSE) at test-process_ontology_files.R:79:3
      2.   └─FAIRmaterials:::process_files(...)
      3.     └─FAIRmaterials:::plot_ontology_tree2(...)
      4.       └─DiagrammeR::render_graph(...)
      5.         └─DiagrammeR:::get_svg_tbl(svg_vec)
      6.           ├─dplyr::bind_cols(dplyr::tibble(index = i, type = "svg"), get_attr_tbl(line))
      7.           │ └─rlang::list2(...)
      8.           └─DiagrammeR:::get_attr_tbl(line)
      9.             ├─base::gsub(...)
     10.             └─base::gsub(gsub("<[a-z]*? ", "", line), "\"", "'", .)
    ── Error ('test-process_ontology_files.R:124:3'): Output files are correctly generated and different with value type inclusion for XRay data ──
    <objectNotFoundError/error/condition>
    Error in `get_attr_tbl(line)`: object '.' not found
    Backtrace:
         ▆
      1. └─FAIRmaterials::process_ontology_files(XRay_test_folder, include_graph_valuetype = TRUE) at test-process_ontology_files.R:124:3
      2.   └─FAIRmaterials:::process_files(...)
      3.     └─FAIRmaterials:::plot_ontology_tree2(...)
      4.       └─DiagrammeR::render_graph(...)
      5.         └─DiagrammeR:::get_svg_tbl(svg_vec)
      6.           ├─dplyr::bind_cols(dplyr::tibble(index = i, type = "svg"), get_attr_tbl(line))
      7.           │ └─rlang::list2(...)
      8.           └─DiagrammeR:::get_attr_tbl(line)
      9.             ├─base::gsub(...)
     10.             └─base::gsub(gsub("<[a-z]*? ", "", line), "\"", "'", .)
    ── Error ('test-process_ontology_files.R:166:3'): The output files are correctly generated for merged data ──
    <objectNotFoundError/error/condition>
    Error in `get_attr_tbl(line)`: object '.' not found
    Backtrace:
         ▆
      1. └─FAIRmaterials::process_ontology_files(...) at test-process_ontology_files.R:166:3
      2.   └─FAIRmaterials:::process_files(...)
      3.     └─FAIRmaterials:::plot_ontology_tree2(...)
      4.       └─DiagrammeR::render_graph(...)
      5.         └─DiagrammeR:::get_svg_tbl(svg_vec)
      6.           ├─dplyr::bind_cols(dplyr::tibble(index = i, type = "svg"), get_attr_tbl(line))
      7.           │ └─rlang::list2(...)
      8.           └─DiagrammeR:::get_attr_tbl(line)
      9.             ├─base::gsub(...)
     10.             └─base::gsub(gsub("<[a-z]*? ", "", line), "\"", "'", .)
    
    [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ]
    Error:
    ! Test failures.
    Execution halted

Package: modeldiagramR
Check: examples
New result: ERROR
  Running examples in ‘modeldiagramR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: SSPD3
  > ### Title: Simulated data for a split-split-plot experimental design.
  > ### Aliases: SSPD3
  > ### Keywords: data design experimental split-split-plot
  > 
  > ### ** Examples
  > 
  > data("SSPD3")
  > 
  > # Simple model for testing
  > library(nlme)
  > lme_simple <- lme(RESP ~ Fungicide + Variety, random=~1|LOCATION/WHOLE_PLOT,
  +                      data=SSPD3)
  > model_diagram(lme_simple)
  Error in get_attr_tbl(line) : object '.' not found
  Calls: model_diagram ... <Anonymous> -> list2 -> get_attr_tbl -> gsub -> gsub
  Execution halted