Check results for 'spant'

using R version 4.5.2 (2025-10-31)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.7.8
using session charset: UTF-8
checking for file ‘spant/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘spant’ version ‘3.7.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘spant’ can be installed ... [7s/8s] OK See the install log for details.
used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
used SDK: ‘MacOSX11.3.1.sdk’
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking whether startup messages can be suppressed ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [9s/9s] OK
checking Rd files ... [1s/1s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking compiled code ... OK
checking usage of KIND in Fortran files ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [0s/0s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [1s/1s] ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(spant) spant 3.7.0 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 ...
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [12s/9s] ERROR Error(s) in re-building vignettes: sh: line 1: 99828 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpCmn2om/file175dc3a59ad05' 2>&1 < '/Volumes/Temp/tmp/RtmpCmn2om/file175dc556e4130' --- 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, 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 (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 30: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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("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/RtmpCmn2om/file175dc3d078b88.rds") An irrecoverable exception occurred. R is aborting now ... sh: line 1: 901 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpCmn2om/file175dc70ed0201' 2>&1 < '/Volumes/Temp/tmp/RtmpCmn2om/file175dc581ec992' --- re-building ‘spant-basis-simulation.Rmd’ using rmarkdown *** caught segfault *** address 0x2, cause 'invalid permissions' Traceback: 1: eigen(H_mat_list$H_mat, symmetric = TRUE) 2: spin_sys(spin_params, ft, ref) 3: pul_seq(group, ft, ref, ...) 4: sim_mol(mol_list[[n]], pul_seq, ft, ref, fs, N, xlim, ...) 5: sim_basis(mol_list, pul_seq = seq_slaser_ideal, acq_paras = def_acq_paras(N = 2048, fs = 2000, ft = 127800000), TE1 = 0.008, TE2 = 0.011, TE3 = 0.009) 6: eval(expr, envir) 7: eval(expr, envir) 8: withVisible(eval(expr, envir)) 9: withCallingHandlers(code, message = function (cnd) { watcher$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$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 29: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 30: process_file(text, output) 31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 33: vweave_rmarkdown(...) 34: engine$weave(file, quiet = quiet, encoding = enc) 35: doTryCatch(return(expr), name, parentenv, handler) 36: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 37: tryCatchList(expr, classes, parentenv, handlers) 38: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 39: tools:::.buildOneVignette("spant-basis-simulation.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-basis-simulation", "UTF-8", "/Volumes/Temp/tmp/RtmpCmn2om/file175dc3979e221.rds") An irrecoverable exception occurred. R is aborting now ... sh: line 1: 1410 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpCmn2om/file175dc1a4a2bb1' 2>&1 < '/Volumes/Temp/tmp/RtmpCmn2om/file175dc7b7a7ef2' --- re-building ‘spant-intro.Rmd’ using rmarkdown 2025-12-08 00:26:20.625 R[1410:575930] XType: Using static font registry. *** caught segfault *** address 0x2, cause 'invalid permissions' Traceback: 1: eigen(H_mat_list$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$ft, lcm_compat = lcm_compat), seq_press_ideal, acq_paras = acq_paras, xlim = xlim, TE1 = TE1, TE2 = TE2) 6: sim_basis_1h_brain_press(mrs_proc) 7: eval(expr, envir) 8: eval(expr, envir) 9: withVisible(eval(expr, envir)) 10: withCallingHandlers(code, message = function (cnd) { watcher$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$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 30: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 31: process_file(text, output) 32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 34: vweave_rmarkdown(...) 35: engine$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 40: tools:::.buildOneVignette("spant-intro.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/spant.Rcheck/vign_test/spant", TRUE, FALSE, "spant-intro", "UTF-8", "/Volumes/Temp/tmp/RtmpCmn2om/file175dc4d43bd70.rds") An irrecoverable exception occurred. R is aborting now ... sh: line 1: 2786 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpCmn2om/file175dc4d9e4f58' 2>&1 < '/Volumes/Temp/tmp/RtmpCmn2om/file175dc546b4237' --- re-building ‘spant-metabolite-simulation.Rmd’ using rmarkdown *** caught segfault *** address 0x3f, cause 'invalid permissions' Traceback: 1: eigen(H_mat_list$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, 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 (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 30: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), 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-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/RtmpCmn2om/file175dc27248133.rds") An irrecoverable exception occurred. R is aborting now ... --- re-building ‘spant-preprocessing.Rmd’ using rmarkdown 2025-12-08 00:26:22.588 R[3643:579275] 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
checking PDF version of manual ... [5s/5s] OK
DONE Status: 2 ERRORs
using check arguments '--no-clean-on-error '