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Last updated on 2026-04-30 11:57:07 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.9.0 | 28.70 | 256.76 | 285.46 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.9.0 | 15.99 | 187.44 | 203.43 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.9.0 | 47.00 | 403.49 | 450.49 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 3.9.0 | 46.00 | 410.88 | 456.88 | OK | |
| r-devel-windows-x86_64 | 3.9.0 | 40.00 | 324.00 | 364.00 | OK | |
| r-patched-linux-x86_64 | 3.9.0 | 30.18 | 249.56 | 279.74 | OK | |
| r-release-linux-x86_64 | 3.9.0 | 26.96 | 247.20 | 274.16 | OK | |
| r-release-macos-arm64 | 3.9.0 | 7.00 | 71.00 | 78.00 | OK | |
| r-release-macos-x86_64 | 3.9.0 | 22.00 | 295.00 | 317.00 | OK | |
| r-release-windows-x86_64 | 3.9.0 | 34.00 | 330.00 | 364.00 | OK | |
| r-oldrel-macos-arm64 | 3.9.0 | 6.00 | 44.00 | 50.00 | ERROR | |
| r-oldrel-macos-x86_64 | 3.9.0 | 23.00 | 636.00 | 659.00 | OK | |
| r-oldrel-windows-x86_64 | 3.9.0 | 50.00 | 400.00 | 450.00 | OK |
Version: 3.9.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(spant)
spant 3.9.0
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: 3.9.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 77380 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a34f1bcee' 2>&1 < '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a6aaac869'
--- 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/RtmpAiJFQO/file1235a51959afa.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 78008 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a41fc548b' 2>&1 < '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a1d129385'
--- 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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
40: tools:::.buildOneVignette("spant-basis-simulation.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-basis-simulation", "UTF-8", "/Volumes/Temp/tmp/RtmpAiJFQO/file1235a724b9c34.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 78317 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a38e9fd17' 2>&1 < '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a9e70e32'
--- re-building ‘spant-intro.Rmd’ using rmarkdown
2026-04-30 18:26:47.675 R[78317:262022] XType: Using static font registry.
*** caught segfault ***
address 0x2, cause 'invalid permissions'
Traceback:
1: eigen(H_mat_list$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
41: tools:::.buildOneVignette("spant-intro.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-intro", "UTF-8", "/Volumes/Temp/tmp/RtmpAiJFQO/file1235a2e930fac.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 79028 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpAiJFQO/file1235a2ad525b3' 2>&1 < '/Volumes/Temp/tmp/RtmpAiJFQO/file1235af9e20bd'
--- re-building ‘spant-metabolite-simulation.Rmd’ using rmarkdown
*** caught segfault ***
address 0x3f, cause 'invalid permissions'
Traceback:
1: eigen(H_mat_list$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/RtmpAiJFQO/file1235a2054f9b2.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘spant-preprocessing.Rmd’ using rmarkdown
2026-04-30 18:26:49.328 R[79437:263780] 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
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