- using R version 4.4.1 Patched (2024-06-25 r86831)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-1) 13.3.0
GNU Fortran (Debian 13.3.0-1) 13.3.0
- 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 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 ... OK
See the install log for details.
- 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 ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [3s/3s] 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 ... [14s/18s] OK
- checking Rd files ... [0s/1s] 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 ... [12s/12s] 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)
librdf error - XML I/O error: Read-only file system
librdf error - XML I/O error: Read-only file system
Error in write_xml.xml_document(xml2::read_xml(svg_code), svg_path) :
Error closing file
Calls: process_ontology_files ... process_files -> <Anonymous> -> write_xml.xml_document
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [30s/32s] ERROR
Running ‘testthat.R’ [30s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(FAIRmaterials)
>
> test_check("FAIRmaterials")
librdf error - XML I/O error: Read-only file system
librdf error - XML I/O error: Read-only file system
librdf error - XML I/O error: Read-only file system
librdf error - XML I/O error: Read-only file system
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-process_ontology_files.R:8:3'): The output files are correctly generated for PV data ──
Error in `write_xml.xml_document(xml2::read_xml(svg_code), svg_path)`: Error closing file
Backtrace:
▆
1. └─FAIRmaterials::process_ontology_files(pv_test_folder, add_external_onto_info = FALSE) at test-process_ontology_files.R:8:3
2. └─FAIRmaterials:::process_files(...)
3. ├─xml2::write_xml(xml2::read_xml(svg_code), svg_path)
4. └─xml2:::write_xml.xml_document(xml2::read_xml(svg_code), svg_path)
── Error ('test-process_ontology_files.R:28:3'): The output files are correctly generated for XRay data ──
Error in `write_xml.xml_document(xml2::read_xml(svg_code), svg_path)`: Error closing file
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(...)
3. ├─xml2::write_xml(xml2::read_xml(svg_code), svg_path)
4. └─xml2:::write_xml.xml_document(xml2::read_xml(svg_code), svg_path)
[ FAIL 2 | WARN 0 | 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 ... [4s/5s] OK
- checking PDF version of manual ... [5s/7s] OK
- checking HTML version of manual ... [0s/0s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs