Last updated on 2026-02-02 07:50:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.2 | 12.84 | 120.06 | 132.90 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.2 | 8.09 | 89.30 | 97.39 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.6.2 | 20.00 | 183.71 | 203.71 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.6.2 | 20.00 | 207.34 | 227.34 | OK | |
| r-devel-windows-x86_64 | 1.6.2 | 19.00 | 127.00 | 146.00 | OK | |
| r-patched-linux-x86_64 | 1.6.2 | 13.57 | 113.03 | 126.60 | OK | |
| r-release-linux-x86_64 | 1.6.2 | 12.01 | 113.11 | 125.12 | OK | |
| r-release-macos-arm64 | 1.6.2 | OK | ||||
| r-release-macos-x86_64 | 1.6.2 | 8.00 | 109.00 | 117.00 | OK | |
| r-release-windows-x86_64 | 1.6.2 | 18.00 | 123.00 | 141.00 | OK | |
| r-oldrel-macos-arm64 | 1.6.2 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.6.2 | 9.00 | 113.00 | 122.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.6.2 | 23.00 | 153.00 | 176.00 | ERROR |
Version: 1.6.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘mdrb’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.6.2
Check: tests
Result: ERROR
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
Flavor: r-oldrel-windows-x86_64