Last updated on 2026-11-12 15:01:11 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 | 5.00 | 130.00 | 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 | 7.00 | 154.00 | 161.00 | 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
2026-11-12 22:16:36.851 R[47673:71133] XType: Using static font registry.
*** 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)
*** caught segfault ***
dcall <- deparse(call, nlines = 1L)address 0x110, cause 'invalid permissions'
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$push(cnd) }
*** caught segfault ***
if (on_message$silence) {address 0x110, cause 'invalid permissions'
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:
*** caught segfault ***
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {address 0x110, cause 'invalid permissions'
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/RtmpDpVMGk/file90d260ea01a0.rds")
An irrecoverable exception occurred. R is aborting now ...
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:
Traceback:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 1: mc.preschedule = TRUE), error = function(e) NULL)RowCumsum(valid)
21: SweepApply(theta, worker, numProcess)
2: 22: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, unlist(SweepApply(theta, worker, numProcess))
23: tieBreak = FALSE, verbose = verbose)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 3: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, E = E, showPlot = TRUE) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)24:
eval(expr, envir) 4: ComputeError(predictions$Observations, predictions$Predictions)
5: 25: eval(expr, envir)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 26: embedded = embedded, validLib = validLib, noTime = noTime, withVisible(eval(expr, envir)) ignoreNan = ignoreNan, backend = backend)$predictions)
27:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 6: FUN(X[[i]], ...){
watcher$capture_plot_and_output() if (on_message$capture) { 7: watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) {lapply(X = S, FUN = FUN, ...)
if (getOption("warn") >= 2 || getOption("warn") < 0) { 8: return()doTryCatch(return(expr), name, parentenv, handler) } watcher$capture_plot_and_output()
9: if (on_warning$capture) { cnd <- sanitize_call(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$push(cnd)
} if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) {10: watcher$capture_plot_and_output()tryCatchList(expr, classes, parentenv, handlers) cnd <- sanitize_call(cnd)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) watcher$push(cnd) if (!is.null(call)) { switch(on_error, continue = invokeRestart("eval_continue"), if (identical(call[[1L]], quote(doTryCatch))) stop = invokeRestart("eval_stop"), error = NULL) call <- sys.call(-4L)}) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]28: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eval(call) if (is.na(w))
29: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(call) type = "b")
if (w > LONG) 30: prefix <- paste0(prefix, "\n ")with_handlers({ } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") for (expr in tle$exprs) { .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) watcher$print_value(ev$value, ev$visible, envir)})
}12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) TRUE
13: }, handlers)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
31: 14: FUN(X[[i]], ...)doWithOneRestart(return(expr), restart)
15: 32: lapply(seq_len(cores), inner.do)withOneRestart(expr, restarts[[1L]])
16: 33: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withRestartList(expr, restarts[-nr])
17: 34: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
35: 18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 36: withRestartList(expr, restarts)
tryCatchList(expr, classes, parentenv, handlers)
37: withRestarts(with_handlers({ for (expr in tle$exprs) {20: ev <- withVisible(eval(expr, envir))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$capture_plot_and_output() mc.preschedule = TRUE), error = function(e) NULL) watcher$print_value(ev$value, ev$visible, envir)
}21: TRUESweepApply(theta, worker, numProcess)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: 22:
Traceback:
evaluate::evaluate(...)unlist(SweepApply(theta, worker, numProcess)) 1:
23: 39: RowCumsum(valid)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", keep_message = if (is.numeric(options$message)) TRUE else options$message, E = E, showPlot = TRUE) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 24:
0Leval(expr, envir)
2: 25: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, eval(expr, envir) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
else 2L tieBreak = FALSE, verbose = verbose)26: }, output_handler = knit_handlers(options$render, options))
withVisible(eval(expr, envir))40:
3: 27: in_dir(input_dir(), expr)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, {41: tau = tau, theta = th, exclusionRadius = exclusionRadius, watcher$capture_plot_and_output()in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (on_message$capture) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd) } keep_message = if (is.numeric(options$message)) TRUE else options$message, embedded = embedded, validLib = validLib, noTime = noTime, stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend) if (options$error && options$include)
0L else 2L 4: }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)ComputeError(predictions$Observations, predictions$Predictions)
43: block_exec(params)
44: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, call_block(x) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
45: process_group(group)
6: 46: if (on_message$silence) {FUN(X[[i]], ...) invokeRestart("muffleMessage")withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }
error = function(e) {}, warning = function (cnd) 7: lapply(X = S, FUN = FUN, ...) if (progress && is.function(pb$interrupt)) { pb$interrupt() if (getOption("warn") >= 2 || getOption("warn") < 0) { if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) 8: return()doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
10: tryCatchList(expr, classes, parentenv, handlers) watcher$capture_plot_and_output()
if (on_warning$capture) {11: tryCatch(expr, error = function(e) { }) cnd <- sanitize_call(cnd)
call <- conditionCall(e) watcher$push(cnd) } if (on_warning$silence) {47: invokeRestart("muffleWarning") }}, error = function (cnd) if (!is.null(call)) {{ if (identical(call[[1L]], quote(doTryCatch))) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") error = function(e) { LONG <- 75L if (progress && is.function(pb$interrupt)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], error <<- format(e) type = "b") if (w > LONG) }), list(rlang_trace_top_env = knit_global()))
watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") cnd <- sanitize_call(cnd)48: } watcher$push(cnd) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), .Internal(seterrmessage(msg[1L])) error = function(e) { switch(on_error, continue = invokeRestart("eval_continue"), if (progress && is.function(pb$interrupt)) stop = invokeRestart("eval_stop"), error = NULL) if (!silent && isTRUE(getOption("show.error.messages"))) { pb$interrupt()}) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) cat(msg, file = outFile) .Internal(printDeferredWarnings()) }), list(rlang_trace_top_env = knit_global())), function(loc) {
}28: eval(call) invisible(structure(msg, class = "try-error", condition = e))
})
setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 29: paste0("\n", rule(), error, "\n", rule()))12: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)eval(call)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
30: with_handlers({13:
49: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))process_file(text, output)
50: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)51: }14: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), FUN(X[[i]], ...) TRUE
output_dir = getwd(), ...)}, handlers)
15: lapply(seq_len(cores), inner.do)
31: 16: 52: vweave_rmarkdown(...)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)53: doWithOneRestart(return(expr), restart)engine$weave(file, quiet = quiet, encoding = enc)
54: 32: doTryCatch(return(expr), name, parentenv, handler)withOneRestart(expr, restarts[[1L]])
55: 33: withRestartList(expr, restarts[-nr])tryCatchOne(expr, names, parentenv, handlers[[1L]])17:
34: doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)56:
tryCatchList(expr, classes, parentenv, handlers)
35: 57: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])18: tryCatch({
tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine$weave(file, quiet = quiet, encoding = enc)
36: setwd(startdir)19: withRestartList(expr, restarts) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {37: texi2pdf(file = output, clean = FALSE, quiet = quiet)withRestarts(with_handlers({tryCatchList(expr, classes, parentenv, handlers) output <- find_vignette_product(name, by = "texi2pdf",
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) engine = engine) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir)20: outputs <- c(outputs, output)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } mc.preschedule = TRUE), error = function(e) NULL)}, error = function(e) { TRUE
thisOK <<- FALSE21: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) fails <<- c(fails, file)SweepApply(theta, worker, numProcess)
38: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
evaluate::evaluate(...) file, conditionMessage(e)))})22:
58: unlist(SweepApply(theta, worker, numProcess))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDpVMGk/file90d260ea01a0.rds")39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
An irrecoverable exception occurred. R is aborting now ...
keep_message = if (is.numeric(options$message)) TRUE else options$message, 23: stop_on_error = if (is.numeric(options$error)) options$error else {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (options$error && options$include) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 0L E = E, showPlot = TRUE) else 2L
24: }, output_handler = knit_handlers(options$render, options))eval(expr, envir)
40: in_dir(input_dir(), expr)25:
eval(expr, envir)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 26: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withVisible(eval(expr, envir)) keep_message = if (is.numeric(options$message)) TRUE else options$message,
27: stop_on_error = if (is.numeric(options$error)) options$error else {withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) if (options$error && options$include) { watcher$capture_plot_and_output() 0L if (on_message$capture) { else 2L watcher$push(cnd) }, output_handler = knit_handlers(options$render, options)))
}42: if (on_message$silence) {eng_r(options)
43: invokeRestart("muffleMessage") }block_exec(params)}, warning = function (cnd) {
44: call_block(x) if (getOption("warn") >= 2 || getOption("warn") < 0) {
45: return()process_group(group) }
46: watcher$capture_plot_and_output()withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (on_warning$capture) { error = function(e) { if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) if (on_warning$silence) { }) invokeRestart("muffleWarning")
}47: }, error = function (cnd) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) 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), 28: eval(call) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()29: eval(call) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)30: }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)with_handlers({ write_utf8(res, output %n% stdout()) for (expr in tle$exprs) { paste0("\nQuitting from ", loc, if (!is.null(error)) ev <- withVisible(eval(expr, envir)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)49: }process_file(text, output) TRUE
}, handlers)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: 51: doWithOneRestart(return(expr), restart)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)32:
52: vweave_rmarkdown(...)
withOneRestart(expr, restarts[[1L]])53:
33: withRestartList(expr, restarts[-nr])engine$weave(file, quiet = quiet, encoding = enc)
34: 54: doWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler)
55: 35: tryCatchOne(expr, names, parentenv, handlers[[1L]])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
56: tryCatchList(expr, classes, parentenv, handlers)
36: 57: withRestartList(expr, restarts)tryCatch({
37: withRestarts(with_handlers({ engine$weave(file, quiet = quiet, encoding = enc) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() setwd(startdir) watcher$print_value(ev$value, ev$visible, envir) output <- find_vignette_product(name, by = "weave", engine = engine) } if (!have.makefile && vignette_is_tex(output)) { TRUE texi2pdf(file = output, clean = FALSE, quiet = quiet)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)38: }evaluate::evaluate(...) outputs <- c(outputs, output)
39: }, error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, thisOK <<- FALSE keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) if (options$error && options$include)
0L58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", else 2L skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDpVMGk/file90d260ea01a0.rds") }, output_handler = knit_handlers(options$render, options))
An irrecoverable exception occurred. R is aborting now ...
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/RtmpDpVMGk/file90d260ea01a0.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