spant

re-building of vignette outputs

Error(s) in re-building vignettes:
sh: line 1: 38769 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmpwb6oPH/file9703511a9e9d' 2>&1 < '/Volumes/Temp/tmp/Rtmpwb6oPH/file97032aa37f04'
--- 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/Rtmpwb6oPH/file97033f7ce74c.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘spant-preprocessing.Rmd’ using rmarkdown
2026-06-29 19:28:04.987 R[38866:203046] XType: Using static font registry.
--- finished re-building ‘spant-preprocessing.Rmd’

SUMMARY: processing the following files failed:
  ‘abfit-baseline-opts.Rmd’ ‘spant-basis-simulation.Rmd’
  ‘spant-intro.Rmd’ ‘spant-metabolite-simulation.Rmd’

Error: Vignette re-building failed.
Execution halted

tests

Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spant)
  spant 4.2.0
  
  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 = parallel, shuffle = shuffle)
  40: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  41: test_check("spant")
  An irrecoverable exception occurred. R is aborting now ...