Last updated on 2026-08-02 13:49:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.3.0 | 29.86 | 256.26 | 286.12 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.3.0 | 18.08 | 187.86 | 205.94 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 4.3.0 | 47.00 | 396.55 | 443.55 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 4.3.0 | 19.00 | 180.14 | 199.14 | OK | |
| r-devel-windows-x86_64 | 4.3.0 | 33.00 | 274.00 | 307.00 | OK | |
| r-patched-linux-x86_64 | 4.3.0 | 27.65 | 250.43 | 278.08 | OK | |
| r-release-linux-x86_64 | 4.3.0 | 24.96 | 255.98 | 280.94 | OK | |
| r-release-macos-arm64 | 4.3.0 | 7.00 | 87.00 | 94.00 | OK | |
| r-release-macos-x86_64 | 4.3.0 | 21.00 | 294.00 | 315.00 | OK | |
| r-release-windows-x86_64 | 4.3.0 | 33.00 | 333.00 | 366.00 | OK | |
| r-oldrel-macos-arm64 | 4.3.0 | 6.00 | 48.00 | 54.00 | ERROR | |
| r-oldrel-macos-x86_64 | 4.3.0 | 21.00 | 269.00 | 290.00 | OK | |
| r-oldrel-windows-x86_64 | 4.3.0 | 44.00 | 405.00 | 449.00 | OK |
Version: 4.3.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp0s8YmZ’ ‘~/tmp/scratch/Rtmp0tsE2B’
‘~/tmp/scratch/Rtmp19QqnC’ ‘~/tmp/scratch/Rtmp1CCBPv’
‘~/tmp/scratch/Rtmp1DlaZE’ ‘~/tmp/scratch/Rtmp1On0BG’
‘~/tmp/scratch/Rtmp2PQJ6T’ ‘~/tmp/scratch/Rtmp2W9UHn’
‘~/tmp/scratch/Rtmp2bwOdm’ ‘~/tmp/scratch/Rtmp3J0sDq’
‘~/tmp/scratch/Rtmp3S36Iu’ ‘~/tmp/scratch/Rtmp3nlLHM’
‘~/tmp/scratch/Rtmp3p2FO2’ ‘~/tmp/scratch/Rtmp4KrVKW’
‘~/tmp/scratch/Rtmp4PTO8v’ ‘~/tmp/scratch/Rtmp5Ni6sU’
‘~/tmp/scratch/Rtmp5ORIxW’ ‘~/tmp/scratch/Rtmp62mITY’
‘~/tmp/scratch/Rtmp6YHF0G’ ‘~/tmp/scratch/Rtmp6e0XLH’
‘~/tmp/scratch/Rtmp7NxwbW’ ‘~/tmp/scratch/Rtmp7ZZsr7’
‘~/tmp/scratch/Rtmp7jMBhd’ ‘~/tmp/scratch/Rtmp7tFYrM’
‘~/tmp/scratch/Rtmp8O1i1z’ ‘~/tmp/scratch/Rtmp8mlU8S’
‘~/tmp/scratch/Rtmp8rvaQX’ ‘~/tmp/scratch/Rtmp94z56D’
‘~/tmp/scratch/Rtmp9TPV0b’ ‘~/tmp/scratch/Rtmp9wKvZS’
‘~/tmp/scratch/RtmpA3k12d’ ‘~/tmp/scratch/RtmpA7BB0g’
‘~/tmp/scratch/RtmpAirnXd’ ‘~/tmp/scratch/RtmpBDE7nE’
‘~/tmp/scratch/RtmpCBclGM’ ‘~/tmp/scratch/RtmpCNwMaj’
‘~/tmp/scratch/RtmpCZLvCn’ ‘~/tmp/scratch/RtmpCx5yfU’
‘~/tmp/scratch/RtmpDFjcUR’ ‘~/tmp/scratch/RtmpDepfv5’
‘~/tmp/scratch/RtmpFoFgbS’ ‘~/tmp/scratch/RtmpGRfxtE’
‘~/tmp/scratch/RtmpGYH2ju’ ‘~/tmp/scratch/RtmpH9IsPa’
‘~/tmp/scratch/RtmpH9rjLY’ ‘~/tmp/scratch/RtmpHitCGL’
‘~/tmp/scratch/RtmpHs9S01’ ‘~/tmp/scratch/RtmpIGVepg’
‘~/tmp/scratch/RtmpJ6W3Ud’ ‘~/tmp/scratch/RtmpJB0NSh’
‘~/tmp/scratch/RtmpJmY68O’ ‘~/tmp/scratch/RtmpKQX6So’
‘~/tmp/scratch/RtmpKRXNwB’ ‘~/tmp/scratch/RtmpKmiYp3’
‘~/tmp/scratch/RtmpLP9pOz’ ‘~/tmp/scratch/RtmpLeVoyg’
‘~/tmp/scratch/RtmpLlmaVb’ ‘~/tmp/scratch/RtmpLrsDMa’
‘~/tmp/scratch/RtmpM2hudM’ ‘~/tmp/scratch/RtmpMDgJem’
‘~/tmp/scratch/RtmpMTzYIg’ ‘~/tmp/scratch/RtmpMdiQUe’
‘~/tmp/scratch/RtmpN5O5Fh’ ‘~/tmp/scratch/RtmpN6NoDT’
‘~/tmp/scratch/RtmpNrg1g9’ ‘~/tmp/scratch/RtmpOzLiNu’
‘~/tmp/scratch/RtmpP3TUeA’ ‘~/tmp/scratch/RtmpP5QPFp’
‘~/tmp/scratch/RtmpPiZ8jU’ ‘~/tmp/scratch/RtmpPjTILn’
‘~/tmp/scratch/RtmpQcHDdv’ ‘~/tmp/scratch/RtmpQzhQ5W’
‘~/tmp/scratch/RtmpRCdvnD’ ‘~/tmp/scratch/RtmpS1iFgx’
‘~/tmp/scratch/RtmpSGVqcM’ ‘~/tmp/scratch/RtmpT5icY8’
‘~/tmp/scratch/RtmpTZxjdI’ ‘~/tmp/scratch/RtmpU5y9rS’
‘~/tmp/scratch/RtmpUag6Nf’ ‘~/tmp/scratch/RtmpUlNscM’
‘~/tmp/scratch/RtmpVGRk9x’ ‘~/tmp/scratch/RtmpVOKrvp’
‘~/tmp/scratch/RtmpVQTmCJ’ ‘~/tmp/scratch/RtmpVuzFxX’
‘~/tmp/scratch/RtmpWbeEyz’ ‘~/tmp/scratch/RtmpWijCQt’
‘~/tmp/scratch/RtmpXdhXwa’ ‘~/tmp/scratch/RtmpYaJSpE’
‘~/tmp/scratch/RtmpZ2wNkr’ ‘~/tmp/scratch/RtmpZfCkkU’
‘~/tmp/scratch/RtmpZrrVu1’ ‘~/tmp/scratch/Rtmpa1ts41’
‘~/tmp/scratch/RtmpaQy3xq’ ‘~/tmp/scratch/Rtmpc4CB59’
‘~/tmp/scratch/RtmpcELtAq’ ‘~/tmp/scratch/RtmpcEcejq’
‘~/tmp/scratch/RtmpcxDjqc’ ‘~/tmp/scratch/RtmpcxLtM3’
‘~/tmp/scratch/Rtmpe3cYVf’ ‘~/tmp/scratch/RtmpeCJaEm’
‘~/tmp/scratch/RtmpeI5j88’ ‘~/tmp/scratch/RtmpeKVp81’
‘~/tmp/scratch/RtmpfOIH5d’ ‘~/tmp/scratch/RtmpfQmEfg’
‘~/tmp/scratch/Rtmpg4OVof’ ‘~/tmp/scratch/RtmpgJ0J71’
‘~/tmp/scratch/RtmpgQwWQB’ ‘~/tmp/scratch/RtmpgRSUq3’
‘~/tmp/scratch/RtmpgvQuji’ ‘~/tmp/scratch/Rtmpi2FheP’
‘~/tmp/scratch/Rtmpi5HIKT’ ‘~/tmp/scratch/RtmpjZLrnr’
‘~/tmp/scratch/RtmpjxHBnw’ ‘~/tmp/scratch/Rtmpk5xJRA’
‘~/tmp/scratch/RtmpkEtG1S’ ‘~/tmp/scratch/RtmpkISMWS’
‘~/tmp/scratch/RtmpkM0adu’ ‘~/tmp/scratch/RtmpkeKGfx’
‘~/tmp/scratch/Rtmpl2fzY6’ ‘~/tmp/scratch/Rtmplfis8C’
‘~/tmp/scratch/RtmpltPKaT’ ‘~/tmp/scratch/RtmpluFfpz’
‘~/tmp/scratch/RtmplysOpU’ ‘~/tmp/scratch/RtmpmaK5a0’
‘~/tmp/scratch/RtmpmrmWg5’ ‘~/tmp/scratch/RtmpmtJzc8’
‘~/tmp/scratch/RtmpnQhBS9’ ‘~/tmp/scratch/RtmpnSBU6R’
‘~/tmp/scratch/Rtmpnre0Y0’ ‘~/tmp/scratch/Rtmpo5ZkLo’
‘~/tmp/scratch/RtmpoG1qPt’ ‘~/tmp/scratch/RtmpoU3Fki’
‘~/tmp/scratch/RtmpokJLGw’ ‘~/tmp/scratch/RtmpozHFIh’
‘~/tmp/scratch/Rtmpp6XXN3’ ‘~/tmp/scratch/RtmppHgcsx’
‘~/tmp/scratch/RtmppiL0wa’ ‘~/tmp/scratch/RtmprqrBKy’
‘~/tmp/scratch/RtmpsGTtwZ’ ‘~/tmp/scratch/Rtmpspe7ke’
‘~/tmp/scratch/RtmptIO8sq’ ‘~/tmp/scratch/RtmptKdYG2’
‘~/tmp/scratch/RtmptW3OmW’ ‘~/tmp/scratch/Rtmptn3NiE’
‘~/tmp/scratch/RtmpuJW9vO’ ‘~/tmp/scratch/RtmpuVCmFQ’
‘~/tmp/scratch/RtmpvWvlJ0’ ‘~/tmp/scratch/RtmpwQGveJ’
‘~/tmp/scratch/RtmpwbVSCY’ ‘~/tmp/scratch/Rtmpwlk2y5’
‘~/tmp/scratch/RtmpwvoWYx’ ‘~/tmp/scratch/RtmpxVfOge’
‘~/tmp/scratch/RtmpxfFmUs’ ‘~/tmp/scratch/RtmpxowARQ’
‘~/tmp/scratch/Rtmpxx0c6e’ ‘~/tmp/scratch/RtmpyNKcAf’
‘~/tmp/scratch/RtmpymWI2P’ ‘~/tmp/scratch/RtmpzQvFJP’
‘~/tmp/scratch/Rtmpzh2Krc’ ‘~/tmp/scratch/RtmpzhP9WJ’
‘~/tmp/scratch/RtmpzzKh3E’ ‘~/tmp/scratch/xvfb-run.08nt2I’
‘~/tmp/scratch/xvfb-run.0Mk150’ ‘~/tmp/scratch/xvfb-run.19VDfP’
‘~/tmp/scratch/xvfb-run.1bilqZ’ ‘~/tmp/scratch/xvfb-run.2zorKD’
‘~/tmp/scratch/xvfb-run.3nWj1B’ ‘~/tmp/scratch/xvfb-run.46amRB’
‘~/tmp/scratch/xvfb-run.4lc4SI’ ‘~/tmp/scratch/xvfb-run.5O7n4m’
‘~/tmp/scratch/xvfb-run.86iTw4’ ‘~/tmp/scratch/xvfb-run.88ucUI’
‘~/tmp/scratch/xvfb-run.8YvkRQ’ ‘~/tmp/scratch/xvfb-run.8uEc82’
‘~/tmp/scratch/xvfb-run.CGmkP5’ ‘~/tmp/scratch/xvfb-run.E3j36D’
‘~/tmp/scratch/xvfb-run.FBY6nx’ ‘~/tmp/scratch/xvfb-run.FNQVA1’
‘~/tmp/scratch/xvfb-run.FaMncu’ ‘~/tmp/scratch/xvfb-run.FyCxBk’
‘~/tmp/scratch/xvfb-run.GTDJk9’ ‘~/tmp/scratch/xvfb-run.H1WM6Q’
‘~/tmp/scratch/xvfb-run.HLMhNC’ ‘~/tmp/scratch/xvfb-run.HoAHs4’
‘~/tmp/scratch/xvfb-run.JFxtvR’ ‘~/tmp/scratch/xvfb-run.JMywix’
‘~/tmp/scratch/xvfb-run.JoiHJw’ ‘~/tmp/scratch/xvfb-run.LIgeGW’
‘~/tmp/scratch/xvfb-run.LpKVk7’ ‘~/tmp/scratch/xvfb-run.MIwKwd’
‘~/tmp/scratch/xvfb-run.Mtac7y’ ‘~/tmp/scratch/xvfb-run.NDzTe3’
‘~/tmp/scratch/xvfb-run.NnLMxE’ ‘~/tmp/scratch/xvfb-run.OCnrmG’
‘~/tmp/scratch/xvfb-run.PdCMkY’ ‘~/tmp/scratch/xvfb-run.Q1pHIj’
‘~/tmp/scratch/xvfb-run.QZKr2X’ ‘~/tmp/scratch/xvfb-run.QhKSgH’
‘~/tmp/scratch/xvfb-run.RJhRZT’ ‘~/tmp/scratch/xvfb-run.TTtaeg’
‘~/tmp/scratch/xvfb-run.TW4UbY’ ‘~/tmp/scratch/xvfb-run.TmZEuw’
‘~/tmp/scratch/xvfb-run.TvVDU1’ ‘~/tmp/scratch/xvfb-run.UKyKcg’
‘~/tmp/scratch/xvfb-run.VhN20y’ ‘~/tmp/scratch/xvfb-run.W36sOr’
‘~/tmp/scratch/xvfb-run.WOrJ3B’ ‘~/tmp/scratch/xvfb-run.X4xheC’
‘~/tmp/scratch/xvfb-run.YRGLmr’ ‘~/tmp/scratch/xvfb-run.Yd3knu’
‘~/tmp/scratch/xvfb-run.a5msR8’ ‘~/tmp/scratch/xvfb-run.d21Ax4’
‘~/tmp/scratch/xvfb-run.dEsNyx’ ‘~/tmp/scratch/xvfb-run.ddEVal’
‘~/tmp/scratch/xvfb-run.glLxjg’ ‘~/tmp/scratch/xvfb-run.grYLAC’
‘~/tmp/scratch/xvfb-run.iFgo3K’ ‘~/tmp/scratch/xvfb-run.lbB7TV’
‘~/tmp/scratch/xvfb-run.n70vrg’ ‘~/tmp/scratch/xvfb-run.oiemZ2’
‘~/tmp/scratch/xvfb-run.pT0BDO’ ‘~/tmp/scratch/xvfb-run.qf1kuN’
‘~/tmp/scratch/xvfb-run.rE2zE8’ ‘~/tmp/scratch/xvfb-run.rN11Mu’
‘~/tmp/scratch/xvfb-run.tBkE9b’ ‘~/tmp/scratch/xvfb-run.unT14d’
‘~/tmp/scratch/xvfb-run.weUKXN’ ‘~/tmp/scratch/xvfb-run.wpqfOi’
‘~/tmp/scratch/xvfb-run.x67BYR’ ‘~/tmp/scratch/xvfb-run.yUbTOl’
‘~/tmp/scratch/xvfb-run.zLJowz’ ‘~/tmp/scratch/xvfb-run.zprP19’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(spant)
spant 4.3.0
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) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
17: test_code(code, parent.frame())
18: test_that("Test data stimulation step", { sim_res <- sim_brain_1h(pul_seq = seq_press_ideal, full_output = TRUE, type = "normal_v1") expect_equal_to_reference(sim_res, "abfit_sim_res.rds", tolerance = 1e-06) set.seed(1) mrs_data <- add_noise(shift(phase(scale_mrs_amp(lb(sim_res$mrs_data, 6), 1/10), 130), 0.1), 0.001, fd = FALSE) expect_equal_to_reference(mrs_data, "abfit_sim_mrs_data.rds", tolerance = 1e-06)})
19: eval(code, test_env)
20: eval(code, test_env)
21: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(expr, restarts[[1L]])
28: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
29: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
30: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
31: FUN(X[[i]], ...)
32: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
37: with_reporter(reporters$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 ...
Flavor: r-oldrel-macos-arm64
Version: 4.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 26967 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpOyA46U/file64fd7c14def0' 2>&1 < '/Volumes/Temp/tmp/RtmpOyA46U/file64fd3e389e34'
--- 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$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestartList(expr, restarts[-nr])
17: doWithOneRestart(return(expr), restart)
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19: withRestartList(expr, restarts)
20: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
23: in_dir(input_dir(), expr)
24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
30: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
31: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = 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("abfit-baseline-opts.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "abfit-baseline-opts", "UTF-8", "/Volumes/Temp/tmp/RtmpOyA46U/file64fd7d0b7882.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 27615 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpOyA46U/file64fd6ecbee09' 2>&1 < '/Volumes/Temp/tmp/RtmpOyA46U/file64fde78c9b3'
--- re-building ‘spant-basis-simulation.Rmd’ using rmarkdown
*** caught segfault ***
address 0x2, cause 'invalid permissions'
Traceback:
1: eigen(H_mat_list$H_mat, symmetric = TRUE)
2: spin_sys(spin_params, ft, ref)
3: pul_seq(group, ft, ref, ...)
4: sim_mol(mol_list[[n]], pul_seq, ft, ref, fs, N, xlim, ...)
5: sim_basis(mol_list, pul_seq = seq_slaser_ideal, acq_paras = def_acq_paras(N = 2048, fs = 2000, ft = 127800000), TE1 = 0.008, TE2 = 0.011, TE3 = 0.009)
6: eval(expr, envir)
7: eval(expr, envir)
8: withVisible(eval(expr, envir))
9: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
10: eval(call)
11: eval(call)
12: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
13: doWithOneRestart(return(expr), restart)
14: withOneRestart(expr, restarts[[1L]])
15: withRestartList(expr, restarts[-nr])
16: doWithOneRestart(return(expr), restart)
17: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
18: withRestartList(expr, restarts)
19: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), expr)
23: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
24: eng_r(options)
25: block_exec(params)
26: call_block(x)
27: process_group(group)
28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
29: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
30: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
31: process_file(text, output)
32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
34: vweave_rmarkdown(...)
35: engine$weave(file, quiet = quiet, encoding = enc)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
40: tools:::.buildOneVignette("spant-basis-simulation.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-basis-simulation", "UTF-8", "/Volumes/Temp/tmp/RtmpOyA46U/file64fd771a87d5.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 28058 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpOyA46U/file64fd4af1c154' 2>&1 < '/Volumes/Temp/tmp/RtmpOyA46U/file64fd45cb983c'
--- re-building ‘spant-intro.Rmd’ using rmarkdown
2026-08-02 20:32:45.963 R[28058:190085] XType: Using static font registry.
*** caught segfault ***
address 0x2, cause 'invalid permissions'
Traceback:
1: eigen(H_mat_list$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$ft, lcm_compat = lcm_compat), seq_press_ideal, acq_paras = acq_paras, xlim = xlim, TE1 = TE1, TE2 = TE2)
6: sim_basis_1h_brain_press(mrs_proc)
7: eval(expr, envir)
8: eval(expr, envir)
9: withVisible(eval(expr, envir))
10: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestartList(expr, restarts[-nr])
17: doWithOneRestart(return(expr), restart)
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19: withRestartList(expr, restarts)
20: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
23: in_dir(input_dir(), expr)
24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
30: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
31: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
41: tools:::.buildOneVignette("spant-intro.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-intro", "UTF-8", "/Volumes/Temp/tmp/RtmpOyA46U/file64fd1c020e31.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 28953 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpOyA46U/file64fd607e2c09' 2>&1 < '/Volumes/Temp/tmp/RtmpOyA46U/file64fd7b7d345c'
--- re-building ‘spant-metabolite-simulation.Rmd’ using rmarkdown
*** caught segfault ***
address 0x3f, cause 'invalid permissions'
Traceback:
1: eigen(H_mat_list$H_mat, symmetric = TRUE)
2: spin_sys(spin_params, ft, ref)
3: pul_seq(group, ft, ref, ...)
4: sim_mol(ins, ft = 3e+08, N = 4096)
5: lb(sim_mol(ins, ft = 3e+08, N = 4096), 2)
6: plot(lb(sim_mol(ins, ft = 3e+08, N = 4096), 2), xlim = c(3.8, 3.1))
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$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestartList(expr, restarts[-nr])
17: doWithOneRestart(return(expr), restart)
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19: withRestartList(expr, restarts)
20: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
23: in_dir(input_dir(), expr)
24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
30: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
31: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = 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/RtmpOyA46U/file64fd3977aef0.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘spant-preprocessing.Rmd’ using rmarkdown
2026-08-02 20:32:47.678 R[29014:191614] 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
Flavor: r-oldrel-macos-arm64