Running 'testthat.R' [16s]
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(metabodecon)
  > 
  > test_check("metabodecon")
  Starting 2 test processes.
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.39 Starting deconvolution of 1 spectrum using 1 worker
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.39 Starting deconvolution of sap_01
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.39 Removing water signal
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.39 Removing negative signals
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.39 Smoothing signals
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 Starting peak selection
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 Detected 24 peaks
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40
  > test-generate_lorentz_curves.R:  Detected 24 peaks
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 Removing peaks with low scores
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 Removed 20 peaks
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 Initializing Lorentz curves
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.40 MSE at peak tiplet positions: 0.0000023352180995647374
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.41 Refining Lorentz Curves
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.41 MSE at peak tiplet positions: 0.0000000822818617368644
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.42 MSE at peak tiplet positions: 0.0000000163050712082373
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.42 MSE at peak tiplet positions: 0.0000000069366441759494
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.43 Formatting return object as decon1
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.43 Finished deconvolution of sap_01
  > test-generate_lorentz_curves.R: 2026-01-31 10:55:23.44 Finished deconvolution of 1 spectrum in 0.045 secs
  > test-as_decon.R: 2026-01-31 10:55:25.41 Starting deconvolution of sap_01
  > test-as_decon.R: 2026-01-31 10:55:25.41
  > test-as_decon.R:  Removing water signal
  > test-as_decon.R: 2026-01-31 10:55:25.41 Removing negative signals
  > test-as_decon.R: 2026-01-31 10:55:25.41 Smoothing signals
  > test-as_decon.R: 2026-01-31 10:55:25.41 Starting peak selection
  > test-as_decon.R: 2026-01-31 10:55:25.41 Detected 18 peaks
  > test-as_decon.R: 2026-01-31 10:55:25.41 Detected 18 peaks
  > test-as_decon.R: 2026-01-31 10:55:25.41 Removing peaks with low scores
  > test-as_decon.R: 2026-01-31 10:55:25.41 Removed 14 peaks
  > test-as_decon.R: 2026-01-31 10:55:25.41 Initializing Lorentz curves
  > test-as_decon.R: 2026-01-31 10:55:25.41 MSE at peak tiplet positions: 0.0000024963648931653171
  > test-as_decon.R: 2026-01-31 10:55:25.42 Refining Lorentz Curves
  > test-as_decon.R: 2026-01-31 10:55:25.42 MSE at peak tiplet positions: 0.0000001165616696457336
  > test-as_decon.R: 2026-01-31 10:55:25.42 MSE at peak tiplet positions: 0.0000000180892220732881
  > test-as_decon.R: 2026-01-31 10:55:25.43 MSE at peak tiplet positions: 0.0000000055685735596686
  > test-as_decon.R: 2026-01-31 10:55:25.43 Formatting return object as idecon
  > test-as_decon.R: 2026-01-31 10:55:25.43 Finished deconvolution of sap_01
  > test-as_decon.R: 2026-01-31 10:55:25.43
  > test-as_decon.R:  Starting deconvolution of sap_01 using Rust backend
  > test-deconvolute.R: 2026-01-31 10:55:26.33 Starting deconvolution of 1 spectrum using 1 worker
  > test-deconvolute.R: 2026-01-31 10:55:26.33 Starting deconvolution of sap_01
  > test-deconvolute.R: 2026-01-31 10:55:26.33
  > test-deconvolute.R:  Removing water signal
  > test-deconvolute.R: 2026-01-31 10:55:26.33 Removing negative signals
  > test-deconvolute.R: 2026-01-31 10:55:26.33 Smoothing signals
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Starting peak selection
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Detected 24 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Detected 24 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Removing peaks with low scores
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Removed 20 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Initializing Lorentz curves
  > test-deconvolute.R: 2026-01-31 10:55:26.34 MSE at peak tiplet positions: 0.0000023352180995647374
  > test-deconvolute.R: 2026-01-31 10:55:26.34 Refining Lorentz Curves
  > test-deconvolute.R: 2026-01-31 10:55:26.35 MSE at peak tiplet positions: 0.0000000822818617368644
  > test-deconvolute.R: 2026-01-31 10:55:26.35 MSE at peak tiplet positions: 0.0000000163050712082373
  > test-deconvolute.R: 2026-01-31 10:55:26.36 MSE at peak tiplet positions: 0.0000000069366441759494
  > test-deconvolute.R: 2026-01-31 10:55:26.36 Formatting return object as decon2
  > test-deconvolute.R: 2026-01-31 10:55:26.37 Finished deconvolution of sap_01
  > test-deconvolute.R: 2026-01-31 10:55:26.37 Finished deconvolution of 1 spectrum in 0.033 secs
  > test-deconvolute.R: 2026-01-31 10:55:26.42 Starting deconvolution of 2 spectra using 1 worker
  > test-deconvolute.R: 2026-01-31 10:55:26.42 Starting deconvolution of sim_01
  > test-deconvolute.R: 2026-01-31 10:55:26.42 Removing water signal
  > test-deconvolute.R: 2026-01-31 10:55:26.42 Removing negative signals
  > test-deconvolute.R: 2026-01-31 10:55:26.42
  > test-deconvolute.R:  Smoothing signals
  > test-deconvolute.R: 2026-01-31 10:55:26.44 Starting peak selection
  > test-deconvolute.R: 2026-01-31 10:55:26.44 Detected 314 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.44
  > test-deconvolute.R:  Detected 314 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.44 Removing peaks with low scores
  > test-deconvolute.R: 2026-01-31 10:55:26.44 Removed 287 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.44 Initializing Lorentz curves
  > test-deconvolute.R: 2026-01-31 10:55:26.44 MSE at peak tiplet positions: 4.0838805770844048836921
  > test-deconvolute.R: 2026-01-31 10:55:26.45 Refining Lorentz Curves
  > test-deconvolute.R: 2026-01-31 10:55:26.45 MSE at peak tiplet positions: 0.1609359876216345797140
  > test-deconvolute.R: 2026-01-31 10:55:26.46 MSE at peak tiplet positions: 0.0228015051613790313556
  > test-deconvolute.R: 2026-01-31 10:55:26.46 MSE at peak tiplet positions: 0.0071638016610617799920
  > test-deconvolute.R: 2026-01-31 10:55:26.47 Formatting return object as decon2
  > test-deconvolute.R: 2026-01-31 10:55:26.48 Finished deconvolution of sim_01
  > test-deconvolute.R: 2026-01-31 10:55:26.48 Starting deconvolution of sim_02
  > test-deconvolute.R: 2026-01-31 10:55:26.48 Removing water signal
  > test-deconvolute.R: 2026-01-31 10:55:26.48 Removing negative signals
  > test-deconvolute.R: 2026-01-31 10:55:26.48 Smoothing signals
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Starting peak selection
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Detected 316 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Detected 316 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Removing peaks with low scores
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Removed 286 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Initializing Lorentz curves
  > test-deconvolute.R: 2026-01-31 10:55:26.50 MSE at peak tiplet positions: 3.8338943428876719465848
  > test-deconvolute.R: 2026-01-31 10:55:26.50 Refining Lorentz Curves
  > test-deconvolute.R: 2026-01-31 10:55:26.51 MSE at peak tiplet positions: 0.1289481941626757499630
  > test-deconvolute.R: 2026-01-31 10:55:26.52 MSE at peak tiplet positions: 0.0135651899090413786964
  > test-deconvolute.R: 2026-01-31 10:55:26.53 MSE at peak tiplet positions: 0.0025556755331531087749
  > test-deconvolute.R: 2026-01-31 10:55:26.53 Formatting return object as decon2
  > test-deconvolute.R: 2026-01-31 10:55:26.55 Finished deconvolution of sim_02
  > test-deconvolute.R: 2026-01-31 10:55:26.55 Finished deconvolution of 2 spectra in 0.13 secs
  > test-deconvolute.R: 2026-01-31 10:55:26.63 Starting deconvolution of 1 spectrum using 1 worker
  > test-deconvolute.R: 2026-01-31 10:55:26.63
  > test-deconvolute.R:  Starting deconvolution of sim_00
  > test-deconvolute.R: 2026-01-31 10:55:26.63 Removing water signal
  > test-deconvolute.R: 2026-01-31 10:55:26.63 Removing negative signals
  > test-deconvolute.R: 2026-01-31 10:55:26.63 Smoothing signals
  > test-deconvolute.R: 2026-01-31 10:55:26.63 Starting peak selection
  > test-deconvolute.R: 2026-01-31 10:55:26.64 Detected 63 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.64 Detected 63 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.64 Removing peaks with low scores
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Starting deconvolution of 1 spectrum using 1 worker
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Starting deconvolution of sim_00
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Removing water signal
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Removing negative signals
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Smoothing signals
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Starting peak selection
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Detected 63 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Detected 63 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Removing peaks with low scores
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Not enough signals found in signal free region. This is a clear indication that the deconvolution parameters are not set correctly. Continuing anyways without dynamic peak filtering, because `force` is TRUE. Note that this might increase runtime drastically.
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Removed 0 peaks
  > test-deconvolute.R: 2026-01-31 10:55:26.66 Initializing Lorentz curves
  > test-deconvolute.R: 2026-01-31 10:55:26.66 MSE at peak tiplet positions: 1.2776621160691834511169
  > test-deconvolute.R: 2026-01-31 10:55:26.67 Refining Lorentz Curves
  > test-deconvolute.R: 2026-01-31 10:55:26.67 MSE at peak tiplet positions: 0.0382680161940291627132
  > test-deconvolute.R: 2026-01-31 10:55:26.69 MSE at peak tiplet positions: 0.0106273721357571498264
  > test-deconvolute.R: 2026-01-31 10:55:26.70 MSE at peak tiplet positions: 0.0050118558740662863191
  > test-deconvolute.R: 2026-01-31 10:55:26.70 Formatting return object as decon2
  > test-deconvolute.R: 2026-01-31 10:55:26.71 Finished deconvolution of sim_00
  > test-deconvolute.R: 2026-01-31 10:55:26.71 Finished deconvolution of 1 spectrum in 0.052 secs
  > test-find_peaks_fast2.R: 2026-01-31 10:55:27.83 Starting peak selection
  > test-find_peaks_fast2.R: 2026-01-31 10:55:27.83 Detected 3 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.39 Starting deconvolution of 2 spectra using 1 worker
  > test-get_si_mat.R: 2026-01-31 10:55:28.39 Starting deconvolution of sim_01
  > test-get_si_mat.R: 2026-01-31 10:55:28.39 Removing water signal
  > test-get_si_mat.R: 2026-01-31 10:55:28.39 Removing negative signals
  > test-get_si_mat.R: 2026-01-31 10:55:28.39 Smoothing signals
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Starting peak selection
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Detected 314 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.41
  > test-get_si_mat.R:  Detected 314 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Removing peaks with low scores
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Removed 287 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Initializing Lorentz curves
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 MSE at peak tiplet positions: 4.0838805770844048836921
  > test-get_si_mat.R: 2026-01-31 10:55:28.41 Refining Lorentz Curves
  > test-get_si_mat.R: 2026-01-31 10:55:28.42 MSE at peak tiplet positions: 0.1609359876216345797140
  > test-get_si_mat.R: 2026-01-31 10:55:28.43 MSE at peak tiplet positions: 0.0228015051613790313556
  > test-get_si_mat.R: 2026-01-31 10:55:28.43 MSE at peak tiplet positions: 0.0071638016610617799920
  > test-get_si_mat.R: 2026-01-31 10:55:28.44 Formatting return object as decon2
  > test-get_si_mat.R: 2026-01-31 10:55:28.45 Finished deconvolution of sim_01
  > test-get_si_mat.R: 2026-01-31 10:55:28.45 Starting deconvolution of sim_02
  > test-get_si_mat.R: 2026-01-31 10:55:28.45 Removing water signal
  > test-get_si_mat.R: 2026-01-31 10:55:28.45 Removing negative signals
  > test-get_si_mat.R: 2026-01-31 10:55:28.45 Smoothing signals
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 Starting peak selection
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 Detected 316 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.47
  > test-get_si_mat.R:  Detected 316 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 Removing peaks with low scores
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 Removed 286 peaks
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 Initializing Lorentz curves
  > test-get_si_mat.R: 2026-01-31 10:55:28.47 MSE at peak tiplet positions: 3.8338943428876719465848
  > test-get_si_mat.R: 2026-01-31 10:55:28.48 Refining Lorentz Curves
  > test-get_si_mat.R: 2026-01-31 10:55:28.48 MSE at peak tiplet positions: 0.1289481941626757499630
  > test-get_si_mat.R: 2026-01-31 10:55:28.49 MSE at peak tiplet positions: 0.0135651899090413786964
  > test-get_si_mat.R: 2026-01-31 10:55:28.50 MSE at peak tiplet positions: 0.0025556755331531087749
  > test-get_si_mat.R: 2026-01-31 10:55:28.50 Formatting return object as decon2
  > test-get_si_mat.R: 2026-01-31 10:55:28.51 Finished deconvolution of sim_02
  > test-get_si_mat.R: 2026-01-31 10:55:28.51 Finished deconvolution of 2 spectra in 0.125 secs
  > test-get_si_mat.R: 2026-01-31 10:55:28.51 All requested packages are already installed.
  > test-get_si_mat.R: 
  > test-get_si_mat.R: 
  > test-get_si_mat.R:  --------------------------------
  > test-get_si_mat.R:  dohCluster will run with maxShift= 50
  > test-get_si_mat.R:  If you want dohCluster to detect the optimal maxShift automatically,
  > test-get_si_mat.R:  use dohCluster(..., maxShift = NULL, ...)
  > test-get_si_mat.R:  --------------------------------
  > test-get_si_mat.R: 
  > test-get_si_mat.R:  aligning spectrum  1
  > test-get_si_mat.R: 
  > test-get_si_mat.R:  Median pearson correlation of aligned spectra:
  > test-get_si_mat.R:  0.9976321
  > test-get_si_mat.R:  Alignment time:  5e-04  minutes
  > test-read_decon_params.R: 
  
  Error:
  ! testthat subprocess exited in file 'test-read_decon_params.R'.
  Caused by error:
  ! R session crashed with exit code -1073741819
  Backtrace:
       ▆
    1. └─testthat::test_check("metabodecon")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─withr::with_dir(...)
    6.         │ └─base::force(code)
    7.         ├─testthat::with_reporter(...)
    8.         │ └─base::tryCatch(...)
    9.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12.         └─testthat:::parallel_event_loop_chunky(queue, reporters, ".")
   13.           └─queue$poll(Inf)
   14.             └─base::lapply(...)
   15.               └─testthat (local) FUN(X[[i]], ...)
   16.                 └─private$handle_error(msg, i)
   17.                   └─cli::cli_abort(...)
   18.                     └─rlang::abort(...)
  Execution halted