spant

Releases

80

Needs compilation

Yes

Needs R

>= 4.1.0

Config/roxygen2/version

8.0.0

Date

2026-10-02

Language

en-GB

• Medical Image Analysis

• Mass spectrometry analysis

re-building of vignette outputs, Error on 1 platform

Error(s) in re-building vignettes:
sh: line 1: 57394 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmprl0lIY/filedc5b5a6d7827' 2>&1 < '/Volumes/Temp/tmp/Rtmprl0lIY/filedc5b48eb76d2'
--- re-building ‘abfit-baseline-opts.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x2, cause 'invalid permissions'

Traceback:
 1: eigen(H_mat_list$H_mat, symmetric = TRUE)
 2: spin_sys(spin_params, ft, ref)
 3: pul_seq(group, ft, ref, ...)
 4: sim_mol(mol_list[[n]], pul_seq, ft, ref, fs, N, xlim, ...)
 5: sim_basis(get_1h_brain_basis_paras(ft = acq_paras$ft, lcm_compat = lcm_compat),     seq_press_ideal, acq_paras = acq_paras, xlim = xlim, TE1 = TE1,     TE2 = TE2)
 6: sim_basis_1h_brain_press(mrs_data)
 7: eval(expr, envir)
 8: eval(expr, envir)
 9: withVisible(eval(expr, envir))
10: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_messa
...[truncated]...
= FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
41: tools:::.buildOneVignette("spant-metabolite-simulation.Rmd",     "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant",     TRUE, FALSE, "spant-metabolite-simulation", "UTF-8", "/Volumes/Temp/tmp/Rtmprl0lIY/filedc5b641cf154.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘spant-preprocessing.Rmd’ using rmarkdown
2026-10-27 21:50:00.394 R[58178:234015] XType: Using static font registry.
--- finished re-building ‘spant-preprocessing
[cut here]

tests, Error on 1 platform

Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spant)
  spant 4.5.0
  
  Attaching package: 'spant'
  
  The following object is masked from 'package:stats':
  
      sd
  
  > 
  > test_check("spant")
  
   *** caught segfault ***
  address 0x2, cause 'invalid permissions'
  
  Traceback:
   1: eigen(H_mat_list$H_mat, symmetric = TRUE)
   2: spin_sys(spin_params, ft, ref)
   3: pul_seq(group, ft, ref, ...)
   4: sim_mol(mol_list[[n]], pul_seq, ft, ref, fs, N, xlim, ...)
   5: sim_basis(brain_basis_paras, pul_seq, acq_paras, xlim = xlim,     ...)
   6: sim_brain_1h(pul_seq = seq_press_ideal, full_output = TRUE, type = "normal_v1")
   7: eval(code, test_env)
   8: eval(code, test_env)
   9: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) { 
...[truncated]...
conditionMessage(cnd), "\n")    NULL})
  37: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  38: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, shuffle = shuffle,     error_call = error_call)
  39: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = 
[cut here]

• abind
• expm
• fields
• graphics
• grDevices
• irlba
• jsonlite
• minpack.lm
• mmand
• nloptr
• numDeriv
• pbapply
• plyr
• pracma
• ptw
• RNifti
• RNiftyReg
• signal
• stringr
• utils

Installing it adds

33 packages, 47.9 MB of source

Of those, need compilation

25

• car
• digest
• divest
• doParallel
• fslr
• ggplot2
• kableExtra
• knitr
• miniUI
• parallel
• ragg
• readxl
• rmarkdown
• rpyANTs
• shiny
• shinyFiles
• testthat
• viridisLite

Lines by kind (42,161)

Lines by language

Languages are counted from file extensions.

Files

517

R functions

679

Compiled functions

12

Object systems

S3: 43 methods

Median

2

Mean

4.74

Highest

149

Median lines per function

15

R functions

679

Calls

1,560

Unconnected

136

Groups

4

Lines counted

13,100

Lines the tests ran

1,900

Tests passed

Yes

Measured with

covr 3.6.5 on R 4.6.1

Has tests

Yes

Test frameworks

testthat

Test cases

9

Lines of tests

133

Test lines per line of code

0

• ABfit baseline options
• Basis simulation
• Common preprocessing steps
• Introduction to spant
• Metabolite simulation

README

No

Release notes file

Yes

Help pages

412

Lines of documentation

11,408

Commits

2,262

Open pull requests

0

Tagged releases

77

Latest tagged release

v4.5.0, 2 Oct 2026

Issues closed in

1 day (median)

Pull requests closed in

1 day (median)

Pull requests merged

100%

Created

15 Nov 2016

Licence file reads as

GPL-3.0

Method, repository practices

Across martin3141

• Bug fix for read_basis_niidir function.
• Added read_fslmrs_json_basis_dir function.
• Added get_gaussian_pulse function to replace the misspelled get_guassian_pulse, which is now deprecated.
• Synced the spant_fit_svs command-line wrapper with fit_svs, adding segment_t1_method, remove_external_basis, pre_align_max_shift, pre_align_ref_freq and pre_align_ref_amp options.
• Added spant_fit_svs_edited command-line wrapper for fit_svs_edited, and install_cli now installs both command-line scripts.
• Fixed the --ecc option in the spant_fit_svs and spant_fit_svs_edited command-line wrappers to default to NULL (auto-detect GE eddy current correction) rather than always forcing FALSE.
• Fixed a broken shebang line in the command-line scripts generated by install_cli, which caused "No such file or directory" errors on Linux.
• Replaced the non-functional tcltk fit_svs_gui() prototype with a working Shiny/miniUI gadget for running fit_svs interactively, and exported it.
• Added spant_fit_svs_gui command-line wrapper to launch fit_svs_gui, installed alongside the other scripts by install_cli.
• Fixed gen_numeric_reg silently overwriting the time column when the name argument was missing. It now stops if name is missing, not a single character string, or equal to "time".
• gen_trap_reg, gen_bold_reg, gen_conv_reg and gen_impulse_reg now stop if trial_type contains "time", which previously created a duplicate time column that was silently dropped by glm_spec.