* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/fioRa.Rcheck’
* using R Under development (unstable) (2026-03-03 r89531)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-03-04 14:49:27 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘fioRa/DESCRIPTION’ ... OK
* this is package ‘fioRa’ version ‘0.3.7’
* 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 whether package ‘fioRa’ can be installed ... OK
* checking package 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 ... [11s/11s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’ [58s/58s]
 [59s/58s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fioRa)
  > 
  > testthat::test_check("fioRa")
  Saving _problems/test-fct_read_fiora-43.R
  Loading required package: shiny
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (3): 'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
    'test-run_script.R:18:3'
  • {vdiffr} is not installed. (2): 'test-app_utils.R:43:5',
    'test-app_utils.R:72:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fct_read_fiora.R:43:3'): fioRa can read the standard fiora example annotated output mgf as Spectra format ──
  Error in `verify_suggested(pkg = c("S4Vectors", "Spectra"))`: The use of this function requires packages S4Vectors, Spectra. Please install.
  Backtrace:
      ▆
   1. └─fioRa::read_fiora(fl = fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Deleting unused snapshots: 'app_utils/plot-spec-standard.svg',
  'app_utils/rendersmiles-kekulise-false.svg', and
  'app_utils/rendersmiles-kekulise-true.svg'
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/fioRa.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:07.22, 115.83 + 9.47