Last updated on 2026-11-12 20:00:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.76 | 227.38 | 231.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.84 | 227.62 | 230.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 174.74 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.27 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.32 | 208.12 | 212.44 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.34 | 211.51 | 214.85 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 4.00 | 131.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 48.00 | 50.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 156.00 | 164.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-13 05:06:39.165 R[47225:76670] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
Traceback:
13: 1: RowCumsum(valid)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 2: FUN(X[[i]], ...)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 15: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(seq_len(cores), inner.do) tieBreak = FALSE, verbose = verbose)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 17: tau = tau, theta = th, exclusionRadius = exclusionRadius, doTryCatch(return(expr), name, parentenv, handler) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4:
ComputeError(predictions$Observations, predictions$Predictions)19:
tryCatchList(expr, classes, parentenv, handlers) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 20: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) mc.preschedule = TRUE), error = function(e) NULL)
6: FUN(X[[i]], ...)21:
SweepApply(theta, worker, numProcess) 7:
lapply(X = S, FUN = FUN, ...)22:
unlist(SweepApply(theta, worker, numProcess)) 8:
doTryCatch(return(expr), name, parentenv, handler)23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 9:
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(expr, envir)
10: 25: tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
11: 26: tryCatch(expr, error = function(e) {withVisible(eval(expr, envir)) call <- conditionCall(e) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 27: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)withCallingHandlers(code, error = function (e) prefix <- paste("Error in", dcall, ": ")rlang::entrace(e), message = function (cnd) LONG <- 75L{ sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_message$capture) { if (is.na(w)) watcher$push(cnd) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") } if (w > LONG) if (on_message$silence) { prefix <- paste0(prefix, "\n ") invokeRestart("muffleMessage") } } else prefix <- "Error : "}, warning = function (cnd) msg <- paste0(prefix, conditionMessage(e), "\n"){ .Internal(seterrmessage(msg[1L])) if (getOption("warn") >= 2 || getOption("warn") < 0) { if (!silent && isTRUE(getOption("show.error.messages"))) { return() cat(msg, file = outFile) } watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) if (on_warning$capture) { } cnd <- sanitize_call(cnd) invisible(structure(msg, class = "try-error", condition = e)) watcher$push(cnd)}) }
if (on_warning$silence) { invokeRestart("muffleWarning")12: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
}, error = function (cnd) 13: {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$capture_plot_and_output()
14: cnd <- sanitize_call(cnd) watcher$push(cnd)FUN(X[[i]], ...) switch(on_error, continue = invokeRestart("eval_continue"),
15: stop = invokeRestart("eval_stop"), error = NULL)lapply(seq_len(cores), inner.do)
})
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)28:
17: eval(call)
doTryCatch(return(expr), name, parentenv, handler)29:
eval(call)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])30:
with_handlers({ for (expr in tle$exprs) {19: ev <- withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
20: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, TRUE mc.preschedule = TRUE), error = function(e) NULL)}, handlers)
21: 31: SweepApply(theta, worker, numProcess)doWithOneRestart(return(expr), restart)
22:
unlist(SweepApply(theta, worker, numProcess))
32: 23: withOneRestart(expr, restarts[[1L]])
Traceback:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 1:
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 33: E = E, showPlot = TRUE)RowCumsum(valid)
withRestartList(expr, restarts[-nr])24:
2: eval(expr, envir)34: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 25: doWithOneRestart(return(expr), restart)eval(expr, envir)
tieBreak = FALSE, verbose = verbose)
3: 35: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])26:
tau = tau, theta = th, exclusionRadius = exclusionRadius, withVisible(eval(expr, envir))36: embedded = embedded, validLib = validLib, noTime = noTime, withRestartList(expr, restarts)
ignoreNan = ignoreNan, backend = backend)
27:
37: 4: withCallingHandlers(code, error = function (e) withRestarts(with_handlers({ComputeError(predictions$Observations, predictions$Predictions)
for (expr in tle$exprs) {rlang::entrace(e), message = function (cnd) 5: { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, watcher$capture_plot_and_output() if (on_message$capture) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, watcher$print_value(ev$value, ev$visible, envir) ignoreNan = ignoreNan, backend = backend)$predictions) watcher$push(cnd) } }
TRUE 6: if (on_message$silence) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)FUN(X[[i]], ...)
invokeRestart("muffleMessage")38: }
evaluate::evaluate(...)}, warning = function (cnd)
{ 7: 39: lapply(X = S, FUN = FUN, ...)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (getOption("warn") >= 2 || getOption("warn") < 0) { 8: keep_message = if (is.numeric(options$message)) TRUE else options$message, doTryCatch(return(expr), name, parentenv, handler) return() stop_on_error = if (is.numeric(options$error)) options$error else { }
watcher$capture_plot_and_output() 9: if (options$error && options$include) if (on_warning$capture) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L cnd <- sanitize_call(cnd)
else 2L watcher$push(cnd) }, output_handler = knit_handlers(options$render, options)) }
10: 40: tryCatchList(expr, classes, parentenv, handlers)in_dir(input_dir(), expr)
if (on_warning$silence) {41: invokeRestart("muffleWarning")11: in_input_dir(evaluate(code, envir = env, new_device = FALSE, }tryCatch(expr, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, call <- conditionCall(e)}, error = function (cnd) if (!is.null(call)) {{ keep_message = if (is.numeric(options$message)) TRUE else options$message, if (identical(call[[1L]], quote(doTryCatch))) watcher$capture_plot_and_output() stop_on_error = if (is.numeric(options$error)) options$error else { call <- sys.call(-4L) if (options$error && options$include) cnd <- sanitize_call(cnd) 0L dcall <- deparse(call, nlines = 1L) else 2L prefix <- paste("Error in", dcall, ": ") watcher$push(cnd) }, output_handler = knit_handlers(options$render, options))) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL) LONG <- 75L42: }) sm <- strsplit(conditionMessage(e), "\n")[[1L]]eng_r(options)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 28: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 43: eval(call)block_exec(params)
type = "b")
29: 44: eval(call) if (w > LONG) call_block(x)
prefix <- paste0(prefix, "\n ")
30: }45: with_handlers({ else prefix <- "Error : "process_group(group) for (expr in tle$exprs) {
msg <- paste0(prefix, conditionMessage(e), "\n") ev <- withVisible(eval(expr, envir)) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {46: cat(msg, file = outFile) watcher$capture_plot_and_output()withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$print_value(ev$value, ev$visible, envir) .Internal(printDeferredWarnings()) } TRUE}, handlers) } error = function(e) { if (progress && is.function(pb$interrupt)) invisible(structure(msg, class = "try-error", condition = e)) pb$interrupt()}) if (is_R_CMD_build() || is_R_CMD_check())
12: error <<- format(e)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) })
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
31: doWithOneRestart(return(expr), restart)
32: 47: withOneRestart(expr, restarts[[1L]])
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 33: error = function(e) {withRestartList(expr, restarts[-nr])
if (progress && is.function(pb$interrupt)) 34:
doWithOneRestart(return(expr), restart) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)35: }), list(rlang_trace_top_env = knit_global()))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 36: error = function(e) {withRestartList(expr, restarts) if (progress && is.function(pb$interrupt))
pb$interrupt()37: withRestarts(with_handlers({ if (is_R_CMD_build() || is_R_CMD_check()) for (expr in tle$exprs) { error <<- format(e) ev <- withVisible(eval(expr, envir)) }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) setwd(wd)15: } write_utf8(res, output %n% stdout()) TRUE paste0("\nQuitting from ", loc, if (!is.null(error)) lapply(seq_len(cores), inner.do)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
16: paste0("\n", rule(), error, "\n", rule()))
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)38: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
evaluate::evaluate(...)
49: 17:
process_file(text, output)39: doTryCatch(return(expr), name, parentenv, handler)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, 50: stop_on_error = if (is.numeric(options$error)) options$error else {18: if (options$error && options$include) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L else 2L
}, output_handler = knit_handlers(options$render, options))51:
19: 40: tryCatchList(expr, classes, parentenv, handlers)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)in_dir(input_dir(), expr)20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
21: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SweepApply(theta, worker, numProcess)
22: keep_message = if (is.numeric(options$message)) TRUE else options$message, unlist(SweepApply(theta, worker, numProcess)) stop_on_error = if (is.numeric(options$error)) options$error else {
52: vweave_rmarkdown(...)23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (options$error && options$include) 0L target = "Thrips_imaginis", lib = "1 73", pred = "1 73", else 2L E = E, showPlot = TRUE)53: }, output_handler = knit_handlers(options$render, options)))
engine$weave(file, quiet = quiet, encoding = enc)42:
eng_r(options)
24: 43: eval(expr, envir)block_exec(params)
44: 25: call_block(x)54:
doTryCatch(return(expr), name, parentenv, handler)45:
process_group(group)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 56: eval(expr, envir) error = function(e) {
tryCatchList(expr, classes, parentenv, handlers)26: if (progress && is.function(pb$interrupt))
pb$interrupt()withVisible(eval(expr, envir))57:
if (is_R_CMD_build() || is_R_CMD_check()) 27: error <<- format(e)tryCatch({ })
withCallingHandlers(code, error = function (e) 47: rlang::entrace(e), message = function (cnd) engine$weave(file, quiet = quiet, encoding = enc){with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(startdir) if (progress && is.function(pb$interrupt)) pb$interrupt() output <- find_vignette_product(name, by = "weave", engine = engine) if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) if (!have.makefile && vignette_is_tex(output)) { if (on_message$capture) { watcher$push(cnd) }), list(rlang_trace_top_env = knit_global())) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)48: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { outputs <- c(outputs, output) }}, error = function(e) { if (on_message$silence) { invokeRestart("muffleMessage") } thisOK <<- FALSE}, warning = function (cnd) fails <<- c(fails, file){ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (getOption("warn") >= 2 || getOption("warn") < 0) { file, conditionMessage(e))) return() if (progress && is.function(pb$interrupt)) }) } pb$interrupt()
watcher$capture_plot_and_output()58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo9eKrk/filea6666b8fcd3b.rds")
An irrecoverable exception occurred. R is aborting now ...
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) if (on_warning$capture) { 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)
49: cnd <- sanitize_call(cnd)process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$push(cnd)
}51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (on_warning$silence) { output_dir = getwd(), ...) 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)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)
38: evaluate::evaluate(...)
39: 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$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: 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()) 52: error <<- format(e)vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc) })
54: 47: doTryCatch(return(expr), name, parentenv, handler)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {55: if (progress && is.function(pb$interrupt)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: pb$interrupt()tryCatchList(expr, classes, parentenv, handlers) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)57: tryCatch({ }), list(rlang_trace_top_env = knit_global())) engine$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)48: output <- find_vignette_product(name, by = "texi2pdf", xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine = engine) error = function(e) { } if (progress && is.function(pb$interrupt)) outputs <- c(outputs, output) pb$interrupt()}, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) thisOK <<- FALSE error <<- format(e) fails <<- c(fails, file) }), list(rlang_trace_top_env = knit_global())), function(loc) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", setwd(wd) file, conditionMessage(e))) 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)
49: 58: process_file(text, output)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
50: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo9eKrk/filea6666b8fcd3b.rds")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
An irrecoverable exception occurred. R is aborting now ...
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo9eKrk/filea6666b8fcd3b.rds")
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: 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)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)
38: evaluate::evaluate(...)
39: 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$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: 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) })
47: 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()))
48: 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)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpo9eKrk/filea6666b8fcd3b.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from rEDM-tutorial.Rmd:466-469 [smap_thrips]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 15, 0
---
Backtrace:
▆
1. └─rEDM::PredictNonlinear(...)
2. └─base::data.frame(Theta = theta, rho = rho)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rEDM-tutorial.Rmd' failed with diagnostics:
arguments imply differing number of rows: 15, 0
--- failed re-building ‘rEDM-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘rEDM-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64