• using R version 4.5.1 (2025-06-13)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• 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 ... INFO Package suggested but not available for checking: ‘Spectra’
• 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 ... [3s/4s] OK See the install log for details.
• checking installed package size ... 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 ... [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 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 ... [3s/4s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... 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 ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [32s/38s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [31s/37s] 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 (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',     'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',     'test-run_script.R:18:3'      ══ 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 package 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 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [6s/13s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '