Last updated on 2026-09-25 03:01:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.27 | 226.93 | 230.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.56 | 231.05 | 233.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.47 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 141.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.72 | 205.17 | 208.89 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.82 | 212.42 | 215.24 | 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 | 6.00 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 54.00 | 56.00 | 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 | 162.00 | 170.00 | 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
2026-09-25 11:19:27.797 R[46160:70047] 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'
*** 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)
Traceback:
9: 1: tryCatchOne(expr, names, parentenv, handlers[[1L]])RowCumsum(valid)
10: 2: tryCatchList(expr, classes, parentenv, handlers)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 11: tieBreak = FALSE, verbose = verbose)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 3: if (!is.null(call)) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (identical(call[[1L]], quote(doTryCatch))) tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- sys.call(-4L) embedded = embedded, validLib = validLib, noTime = noTime, dcall <- deparse(call, nlines = 1L) ignoreNan = ignoreNan, backend = backend) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 4: sm <- strsplit(conditionMessage(e), "\n")[[1L]]ComputeError(predictions$Observations, predictions$Predictions) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 5: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, type = "b") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (w > LONG) embedded = embedded, validLib = validLib, noTime = noTime, prefix <- paste0(prefix, "\n ") ignoreNan = ignoreNan, backend = backend)$predictions) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 6: FUN(X[[i]], ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 7: .Internal(printDeferredWarnings())lapply(X = S, FUN = FUN, ...) }
invisible(structure(msg, class = "try-error", condition = e)) 8: })doTryCatch(return(expr), name, parentenv, handler)
12: 9: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: 10: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
14: 11: FUN(X[[i]], ...)tryCatch(expr, error = function(e) {
call <- conditionCall(e)15: if (!is.null(call)) {lapply(seq_len(cores), inner.do) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)16: dcall <- deparse(call, nlines = 1L)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L17: sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
18: if (is.na(w)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 19: type = "b")tryCatchList(expr, classes, parentenv, handlers) if (w > LONG)
prefix <- paste0(prefix, "\n ")20: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))21: if (!silent && isTRUE(getOption("show.error.messages"))) {SweepApply(theta, worker, numProcess) cat(msg, file = outFile)
.Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))22: unlist(SweepApply(theta, worker, numProcess))})
12: 23: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 13: E = E, showPlot = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: 14: eval(expr, envir)FUN(X[[i]], ...)
15: 25: lapply(seq_len(cores), inner.do)eval(expr, envir)
16: 26: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withVisible(eval(expr, envir))
17: doTryCatch(return(expr), name, parentenv, handler)27:
withCallingHandlers(code, error = function (e) 18: rlang::entrace(e), message = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]]){
watcher$capture_plot_and_output()19: if (on_message$capture) {tryCatchList(expr, classes, parentenv, handlers) watcher$push(cnd)
}20: if (on_message$silence) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, invokeRestart("muffleMessage") mc.preschedule = TRUE), error = function(e) NULL) }
}, warning = function (cnd) 21: {SweepApply(theta, worker, numProcess) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()22: }unlist(SweepApply(theta, worker, numProcess)) watcher$capture_plot_and_output() if (on_warning$capture) {
cnd <- sanitize_call(cnd)23: watcher$push(cnd)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", } target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) if (on_warning$silence) {
invokeRestart("muffleWarning")24: }eval(expr, envir)}, error = function (cnd)
{25: watcher$capture_plot_and_output()eval(expr, envir) cnd <- sanitize_call(cnd)
watcher$push(cnd)26: switch(on_error, continue = invokeRestart("eval_continue"), withVisible(eval(expr, envir)) stop = invokeRestart("eval_stop"), error = NULL)
})27: withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 28: {eval(call) watcher$capture_plot_and_output()
if (on_message$capture) {29: watcher$push(cnd)eval(call) }
if (on_message$silence) {30: invokeRestart("muffleMessage")with_handlers({ } for (expr in tle$exprs) {}, warning = function (cnd) ev <- withVisible(eval(expr, envir)){ watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$print_value(ev$value, ev$visible, envir) return() } } TRUE watcher$capture_plot_and_output()}, handlers) if (on_warning$capture) {
cnd <- sanitize_call(cnd)31: watcher$push(cnd)doWithOneRestart(return(expr), restart) }
32: if (on_warning$silence) {withOneRestart(expr, restarts[[1L]]) invokeRestart("muffleWarning")
}33: }, error = function (cnd) withRestartList(expr, restarts[-nr]){
watcher$capture_plot_and_output()34: cnd <- sanitize_call(cnd)doWithOneRestart(return(expr), restart) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 35: stop = invokeRestart("eval_stop"), error = NULL)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])})
36:
withRestartList(expr, restarts)28:
37: eval(call)withRestarts(with_handlers({
for (expr in tle$exprs) {29: ev <- withVisible(eval(expr, envir))eval(call) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
}30: with_handlers({ TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))38: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)evaluate::evaluate(...) }
TRUE39: }, handlers)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {31: if (options$error && options$include) doWithOneRestart(return(expr), restart) 0L
else 2L }, output_handler = knit_handlers(options$render, options))32:
withOneRestart(expr, restarts[[1L]])40:
in_dir(input_dir(), expr)33:
withRestartList(expr, restarts[-nr])41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 34: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, doWithOneRestart(return(expr), restart) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {35: if (options$error && options$include) 0LwithOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) else 2L
}, output_handler = knit_handlers(options$render, options)))36:
withRestartList(expr, restarts)42:
eng_r(options)37:
withRestarts(with_handlers({43: for (expr in tle$exprs) {block_exec(params)
ev <- withVisible(eval(expr, envir))44: watcher$capture_plot_and_output()call_block(x) watcher$print_value(ev$value, ev$visible, envir)
}45: TRUEprocess_group(group)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
46: 38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), evaluate::evaluate(...) error = function(e) {
if (progress && is.function(pb$interrupt)) 39: pb$interrupt()evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (is_R_CMD_build() || is_R_CMD_check()) keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { }) if (options$error && options$include)
0L else 2L47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options)) error = function(e) {
if (progress && is.function(pb$interrupt)) 40: pb$interrupt()in_dir(input_dir(), expr) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)41: }), list(rlang_trace_top_env = knit_global()))in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 48: keep_message = if (is.numeric(options$message)) TRUE else options$message, xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop_on_error = if (is.numeric(options$error)) options$error else { error = function(e) { if (options$error && options$include) if (progress && is.function(pb$interrupt)) 0L pb$interrupt() else 2L if (is_R_CMD_build() || is_R_CMD_check()) }, output_handler = knit_handlers(options$render, options))) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {42: setwd(wd)eng_r(options) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 43: paste0("\n", rule(), error, "\n", rule()))block_exec(params)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
44: call_block(x)49: process_file(text, output)
45: process_group(group)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 51: error = function(e) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (progress && is.function(pb$interrupt)) output_dir = getwd(), ...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 52: error <<- format(e)vweave_rmarkdown(...)
})53:
engine$weave(file, quiet = quiet, encoding = enc)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 54: error = function(e) {doTryCatch(return(expr), name, parentenv, handler) if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 55: error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), list(rlang_trace_top_env = knit_global()))
56:
tryCatchList(expr, classes, parentenv, handlers)48:
57: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) error = function(e) { setwd(startdir) if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "weave", engine = engine) pb$interrupt() if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) texi2pdf(file = output, clean = FALSE, quiet = quiet) error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", }), list(rlang_trace_top_env = knit_global())), function(loc) { engine = engine) } setwd(wd) outputs <- c(outputs, output)}, error = function(e) { write_utf8(res, output %n% stdout()) thisOK <<- FALSE paste0("\nQuitting from ", loc, if (!is.null(error)) fails <<- c(fails, file) paste0("\n", rule(), error, "\n", rule())) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) file, conditionMessage(e)))
})49:
process_file(text, output)58:
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/RtmpCk5dDa/file952a28bcd1e9.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/RtmpCk5dDa/file952a28bcd1e9.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: 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)
Traceback:
{ 1: watcher$capture_plot_and_output()RowCumsum(valid) if (on_message$capture) {
watcher$push(cnd) 2: }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (on_message$silence) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, invokeRestart("muffleMessage") tieBreak = FALSE, verbose = verbose)
} 3: }, warning = function (cnd) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, { tau = tau, theta = th, exclusionRadius = exclusionRadius, if (getOption("warn") >= 2 || getOption("warn") < 0) { embedded = embedded, validLib = validLib, noTime = noTime, return() ignoreNan = ignoreNan, backend = backend) } watcher$capture_plot_and_output()
if (on_warning$capture) { 4: cnd <- sanitize_call(cnd)ComputeError(predictions$Observations, predictions$Predictions) watcher$push(cnd)
} 5: if (on_warning$silence) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, invokeRestart("muffleWarning") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } embedded = embedded, validLib = validLib, noTime = noTime, }, error = function (cnd) ignoreNan = ignoreNan, backend = backend)$predictions){
watcher$capture_plot_and_output() 6: cnd <- sanitize_call(cnd)FUN(X[[i]], ...) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 7: stop = invokeRestart("eval_stop"), error = NULL)lapply(X = S, FUN = FUN, ...)})
8: 28: doTryCatch(return(expr), name, parentenv, handler)eval(call)
9: 29: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)
10: 30: with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))11: tryCatch(expr, error = function(e) { watcher$capture_plot_and_output() call <- conditionCall(e) if (!is.null(call)) { watcher$print_value(ev$value, ev$visible, envir) if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) TRUE dcall <- deparse(call, nlines = 1L)}, handlers) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L31: sm <- strsplit(conditionMessage(e), "\n")[[1L]]doWithOneRestart(return(expr), restart) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
32: withOneRestart(expr, restarts[[1L]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 33: type = "b")withRestartList(expr, restarts[-nr]) if (w > LONG)
prefix <- paste0(prefix, "\n ")34: }doWithOneRestart(return(expr), restart) else prefix <- "Error : "
35: msg <- paste0(prefix, conditionMessage(e), "\n")withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {36: cat(msg, file = outFile)withRestartList(expr, restarts)
37: .Internal(printDeferredWarnings())withRestarts(with_handlers({ } for (expr in tle$exprs) { invisible(structure(msg, class = "try-error", condition = e)) ev <- withVisible(eval(expr, envir))}) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)12: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))38:
evaluate::evaluate(...)14:
FUN(X[[i]], ...)39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 15: lapply(seq_len(cores), inner.do) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {16: if (options$error && options$include) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 0L
else 2L17: }, output_handler = knit_handlers(options$render, options))doTryCatch(return(expr), name, parentenv, handler)
40: 18: in_dir(input_dir(), expr)tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: 19: in_input_dir(evaluate(code, envir = env, new_device = FALSE, tryCatchList(expr, classes, parentenv, handlers) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 20: stop_on_error = if (is.numeric(options$error)) options$error else {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (options$error && options$include) mc.preschedule = TRUE), error = function(e) NULL) 0L
else 2L21: }, output_handler = knit_handlers(options$render, options)))SweepApply(theta, worker, numProcess)
42: 22: eng_r(options)unlist(SweepApply(theta, worker, numProcess))
43: 23: block_exec(params)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 44: E = E, showPlot = TRUE)call_block(x)
24: eval(expr, envir)45:
process_group(group)25:
eval(expr, envir)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 26: error = function(e) {withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt))
pb$interrupt()27: withCallingHandlers(code, error = function (e) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)rlang::entrace(e), message = function (cnd) }){
watcher$capture_plot_and_output()47: if (on_message$capture) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) error = function(e) { } if (progress && is.function(pb$interrupt)) if (on_message$silence) { pb$interrupt() invokeRestart("muffleMessage") if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e)}, warning = function (cnd) { }), list(rlang_trace_top_env = knit_global())) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()48: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() error = function(e) { if (on_warning$capture) { 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) { }), list(rlang_trace_top_env = knit_global())), function(loc) { invokeRestart("muffleWarning") setwd(wd) write_utf8(res, output %n% stdout()) }}, error = function (cnd) { paste0("\nQuitting from ", loc, if (!is.null(error)) watcher$capture_plot_and_output() paste0("\n", rule(), error, "\n", rule())) cnd <- sanitize_call(cnd)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
watcher$push(cnd)49: switch(on_error, continue = invokeRestart("eval_continue"), process_file(text, output) stop = invokeRestart("eval_stop"), error = NULL)
})50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)28:
eval(call)51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
29: 52: eval(call)
vweave_rmarkdown(...)30: with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))53: watcher$capture_plot_and_output()engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir)
}54: TRUEdoTryCatch(return(expr), name, parentenv, handler)}, handlers)
55: 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])doWithOneRestart(return(expr), restart)
56: 32: tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
57: 33: tryCatch({withRestartList(expr, restarts[-nr]) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)34: output <- find_vignette_product(name, by = "weave", engine = engine)doWithOneRestart(return(expr), restart) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)35: output <- find_vignette_product(name, by = "texi2pdf", withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) engine = engine)
}36: outputs <- c(outputs, output)withRestartList(expr, restarts)}, error = function(e) {
thisOK <<- FALSE37: withRestarts(with_handlers({ fails <<- c(fails, file) for (expr in tle$exprs) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", ev <- withVisible(eval(expr, envir)) file, conditionMessage(e))) watcher$capture_plot_and_output()}) watcher$print_value(ev$value, ev$visible, envir)
}58: TRUEtools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpCk5dDa/file952a28bcd1e9.rds")38:
evaluate::evaluate(...)An irrecoverable exception occurred. R is aborting now ...
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/RtmpCk5dDa/file952a28bcd1e9.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