Last updated on 2026-10-05 19:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.06 | 225.28 | 228.34 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.71 | 224.24 | 226.95 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.52 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.10 | 210.00 | 214.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 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 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 32.00 | 34.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 9.00 | 161.00 | 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
2026-10-06 03:44:45.020 R[46244:68831] 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)
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]], ...)
Traceback:
15: 1: lapply(seq_len(cores), inner.do)
RowCumsum(valid)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 2:
17: doTryCatch(return(expr), name, parentenv, handler)
18: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
19: tieBreak = FALSE, verbose = verbose)tryCatchList(expr, classes, parentenv, handlers)
20: 3: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, mc.preschedule = TRUE), error = function(e) NULL) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 21: ignoreNan = ignoreNan, backend = backend)SweepApply(theta, worker, numProcess)
4:
22: ComputeError(predictions$Observations, predictions$Predictions)unlist(SweepApply(theta, worker, numProcess))
23: 5:
Traceback:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 1: E = E, showPlot = TRUE)RowCumsum(valid) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 2: 24: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)$predictions) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, eval(expr, envir)
tieBreak = FALSE, verbose = verbose) 6: 25:
FUN(X[[i]], ...)eval(expr, envir)
3:
7: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, lapply(X = S, FUN = FUN, ...)26: tau = tau, theta = th, exclusionRadius = exclusionRadius, withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) 8:
doTryCatch(return(expr), name, parentenv, handler)27: withCallingHandlers(code, error = function (e) 4:
rlang::entrace(e), message = function (cnd) ComputeError(predictions$Observations, predictions$Predictions) 9: {tryCatchOne(expr, names, parentenv, handlers[[1L]])
watcher$capture_plot_and_output()
if (on_message$capture) {10: tryCatchList(expr, classes, parentenv, handlers) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, watcher$push(cnd) } knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (on_message$silence) {
embedded = embedded, validLib = validLib, noTime = noTime, invokeRestart("muffleMessage")11: } ignoreNan = ignoreNan, backend = backend)$predictions)}, warning = function (cnd) {
if (getOption("warn") >= 2 || getOption("warn") < 0) { 6: return()tryCatch(expr, error = function(e) {FUN(X[[i]], ...) } watcher$capture_plot_and_output() if (on_warning$capture) {
7: cnd <- sanitize_call(cnd) call <- conditionCall(e) watcher$push(cnd)lapply(X = S, FUN = FUN, ...)
} if (!is.null(call)) { 8: if (on_warning$silence) { invokeRestart("muffleWarning") if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler) }}, error = function (cnd)
{ watcher$capture_plot_and_output() 9: cnd <- sanitize_call(cnd) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL) prefix <- paste("Error in", dcall, ": ")10: LONG <- 75L})tryCatchList(expr, classes, parentenv, handlers)
sm <- strsplit(conditionMessage(e), "\n")[[1L]]28:
eval(call)11:
tryCatch(expr, error = function(e) {29: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") call <- conditionCall(e)eval(call) if (!is.null(call)) { if (is.na(w)) if (identical(call[[1L]], quote(doTryCatch))) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) type = "b")
prefix <- paste("Error in", dcall, ": ") if (w > LONG) LONG <- 75L30:
Traceback:
sm <- strsplit(conditionMessage(e), "\n")[[1L]]with_handlers({ prefix <- paste0(prefix, "\n ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } for (expr in tle$exprs) { else prefix <- "Error : " 1: msg <- paste0(prefix, conditionMessage(e), "\n") ev <- withVisible(eval(expr, envir))RowCumsum(valid) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
watcher$print_value(ev$value, ev$visible, envir) 2: type = "b") .Internal(seterrmessage(msg[1L])) if (w > LONG) }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (!silent && isTRUE(getOption("show.error.messages"))) { prefix <- paste0(prefix, "\n ") TRUE validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) cat(msg, file = outFile)}, handlers) .Internal(printDeferredWarnings()) }
31: doWithOneRestart(return(expr), restart) } 3: else prefix <- "Error : " invisible(structure(msg, class = "try-error", condition = e))
msg <- paste0(prefix, conditionMessage(e), "\n")32: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, withOneRestart(expr, restarts[[1L]]) .Internal(seterrmessage(msg[1L]))}) if (!silent && isTRUE(getOption("show.error.messages"))) { tau = tau, theta = th, exclusionRadius = exclusionRadius,
33: cat(msg, file = outFile) embedded = embedded, validLib = validLib, noTime = noTime, .Internal(printDeferredWarnings()) ignoreNan = ignoreNan, backend = backend)withRestartList(expr, restarts[-nr]) }
invisible(structure(msg, class = "try-error", condition = e)) 4: })
ComputeError(predictions$Observations, predictions$Predictions)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 34: 12: 5: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, doWithOneRestart(return(expr), restart)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 35: ignoreNan = ignoreNan, backend = backend)$predictions)14: 14: FUN(X[[i]], ...)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])FUN(X[[i]], ...)
6: 15: FUN(X[[i]], ...)
lapply(seq_len(cores), inner.do)15: 7:
lapply(X = S, FUN = FUN, ...)lapply(seq_len(cores), inner.do)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)36:
17: 8: 16: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withRestartList(expr, restarts)
17:
18: 37: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestarts(with_handlers({
9: for (expr in tle$exprs) {18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatchOne(expr, names, parentenv, handlers[[1L]]) ev <- withVisible(eval(expr, envir))
19: 10: watcher$capture_plot_and_output()19: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
watcher$print_value(ev$value, ev$visible, envir)20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }20: mc.preschedule = TRUE), error = function(e) NULL) TRUE11: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
tryCatch(expr, error = function(e) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) mc.preschedule = TRUE), error = function(e) NULL)21:
call <- conditionCall(e)SweepApply(theta, worker, numProcess)21:
SweepApply(theta, worker, numProcess)22:
38: if (!is.null(call)) {unlist(SweepApply(theta, worker, numProcess))22: unlist(SweepApply(theta, worker, numProcess))evaluate::evaluate(...) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)23: dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
39: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 23: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, E = E, showPlot = TRUE) keep_message = if (is.numeric(options$message)) TRUE else options$message,
LONG <- 75LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 24: stop_on_error = if (is.numeric(options$error)) options$error else {eval(expr, envir)
if (options$error && options$include) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 25: E = E, showPlot = TRUE) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 0L else 2L }, output_handler = knit_handlers(options$render, options))
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")40: if (is.na(w)) 24: in_dir(input_dir(), expr)eval(expr, envir)
41: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(expr, envir)
type = "b")in_input_dir(evaluate(code, envir = env, new_device = FALSE, 26:
withVisible(eval(expr, envir)) if (w > LONG) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
prefix <- paste0(prefix, "\n ")25: keep_message = if (is.numeric(options$message)) TRUE else options$message, eval(expr, envir)27: } stop_on_error = if (is.numeric(options$error)) options$error else { else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") if (options$error && options$include) .Internal(seterrmessage(msg[1L]))withCallingHandlers(code, error = function (e) 26: if (!silent && isTRUE(getOption("show.error.messages"))) {rlang::entrace(e), message = function (cnd) 0L else 2LwithVisible(eval(expr, envir)) }, output_handler = knit_handlers(options$render, options))){ cat(msg, file = outFile)
watcher$capture_plot_and_output() .Internal(printDeferredWarnings())42:
} invisible(structure(msg, class = "try-error", condition = e)) if (on_message$capture) {eng_r(options) watcher$push(cnd)})
}43: if (on_message$silence) {block_exec(params) invokeRestart("muffleMessage")27:
}withCallingHandlers(code, error = function (e) 12: }, warning = function (cnd) rlang::entrace(e), message = function (cnd) try(lapply(X = S, FUN = FUN, ...), silent = TRUE){{
if (getOption("warn") >= 2 || getOption("warn") < 0) {
watcher$capture_plot_and_output() return() if (on_message$capture) {13: } watcher$push(cnd)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$capture_plot_and_output() } if (on_message$silence) {
44: if (on_warning$capture) {14: call_block(x) cnd <- sanitize_call(cnd) invokeRestart("muffleMessage")
watcher$push(cnd) }45: process_group(group)FUN(X[[i]], ...)
}, warning = function (cnd) }
{46: if (getOption("warn") >= 2 || getOption("warn") < 0) {15: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), lapply(seq_len(cores), inner.do) return() error = function(e) {
if (progress && is.function(pb$interrupt)) }16: pb$interrupt() watcher$capture_plot_and_output()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (on_warning$capture) { if (is_R_CMD_build() || is_R_CMD_check()) cnd <- sanitize_call(cnd) if (on_warning$silence) { error <<- format(e) watcher$push(cnd)
}) invokeRestart("muffleWarning")
17: 47: doTryCatch(return(expr), name, parentenv, handler) }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }
error = function(e) { if (on_warning$silence) {18: if (progress && is.function(pb$interrupt)) }, error = function (cnd) pb$interrupt() invokeRestart("muffleWarning")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is_R_CMD_build() || is_R_CMD_check()) { } watcher$capture_plot_and_output()}, error = function (cnd)
error <<- format(e)19: { cnd <- sanitize_call(cnd)tryCatchList(expr, classes, parentenv, handlers)
watcher$push(cnd) }), list(rlang_trace_top_env = knit_global()))20: switch(on_error, continue = invokeRestart("eval_continue"),
watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 48: stop = invokeRestart("eval_stop"), error = NULL) cnd <- sanitize_call(cnd)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), mc.preschedule = TRUE), error = function(e) NULL) watcher$push(cnd) error = function(e) {})
if (progress && is.function(pb$interrupt)) 21:
switch(on_error, continue = invokeRestart("eval_continue"), SweepApply(theta, worker, numProcess) stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)22:
unlist(SweepApply(theta, worker, numProcess)) pb$interrupt()
29: 23: if (is_R_CMD_build() || is_R_CMD_check()) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", error <<- format(e)eval(call) }), list(rlang_trace_top_env = knit_global())), function(loc) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 28:
E = E, showPlot = TRUE)eval(call)
setwd(wd)
24: write_utf8(res, output %n% stdout())29: eval(expr, envir)30:
paste0("\nQuitting from ", loc, if (!is.null(error)) 25: with_handlers({eval(call)eval(expr, envir) paste0("\n", rule(), error, "\n", rule()))
for (expr in tle$exprs) {26: 30: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withVisible(eval(expr, envir))with_handlers({ ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) { watcher$capture_plot_and_output()
ev <- withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir)49: process_file(text, output) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)27:
}50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) TRUEwithCallingHandlers(code, error = function (e) }
rlang::entrace(e), message = function (cnd) }, handlers)51: {
watcher$capture_plot_and_output()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 31: TRUEdoWithOneRestart(return(expr), restart)}, handlers) output_dir = getwd(), ...)
31: 32: if (on_message$capture) {withOneRestart(expr, restarts[[1L]])doWithOneRestart(return(expr), restart)52:
vweave_rmarkdown(...)33: 32:
withOneRestart(expr, restarts[[1L]])withRestartList(expr, restarts[-nr]) watcher$push(cnd)
53: engine$weave(file, quiet = quiet, encoding = enc)33: 34: withRestartList(expr, restarts[-nr])
doWithOneRestart(return(expr), restart) }54: 34:
if (on_message$silence) {doTryCatch(return(expr), name, parentenv, handler)35: doWithOneRestart(return(expr), restart)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
invokeRestart("muffleMessage")36: 55: 35: }withRestartList(expr, restarts)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
tryCatchOne(expr, names, parentenv, handlers[[1L]])}, warning = function (cnd) 37:
withRestarts(with_handlers({
{ for (expr in tle$exprs) {56: 36: ev <- withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) {withRestartList(expr, restarts)
return() watcher$capture_plot_and_output() }
37: watcher$print_value(ev$value, ev$visible, envir)withRestarts(with_handlers({ } watcher$capture_plot_and_output()57: for (expr in tle$exprs) {tryCatch({ if (on_warning$capture) { ev <- withVisible(eval(expr, envir)) TRUE watcher$capture_plot_and_output() engine$weave(file, quiet = quiet, encoding = enc)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$print_value(ev$value, ev$visible, envir)
}38: cnd <- sanitize_call(cnd) TRUEevaluate::evaluate(...) setwd(startdir)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
39: output <- find_vignette_product(name, by = "weave", engine = engine)38: watcher$push(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }evaluate::evaluate(...) if (!have.makefile && vignette_is_tex(output)) { if (on_warning$silence) {
keep_message = if (is.numeric(options$message)) TRUE else options$message, invokeRestart("muffleWarning")39: texi2pdf(file = output, clean = FALSE, quiet = quiet) } stop_on_error = if (is.numeric(options$error)) options$error else {}, error = function (cnd) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) { 0L output <- find_vignette_product(name, by = "texi2pdf", watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message, else 2L engine = engine) }, output_handler = knit_handlers(options$render, options)) cnd <- sanitize_call(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd)
} switch(on_error, continue = invokeRestart("eval_continue"), if (options$error && options$include) 40: in_dir(input_dir(), expr) outputs <- c(outputs, output) 0L
stop = invokeRestart("eval_stop"), error = NULL) else 2L }, output_handler = knit_handlers(options$render, options))}, error = function(e) {41:
thisOK <<- FALSE40: in_input_dir(evaluate(code, envir = env, new_device = FALSE, })in_dir(input_dir(), expr) fails <<- c(fails, file)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 28: 41: file, conditionMessage(e))) keep_message = if (is.numeric(options$message)) TRUE else options$message, })in_input_dir(evaluate(code, envir = env, new_device = FALSE,
stop_on_error = if (is.numeric(options$error)) options$error else {58: eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (options$error && options$include) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWNAE3F/file839c28fbe291.rds")
keep_message = if (is.numeric(options$message)) TRUE else options$message, 0LAn irrecoverable exception occurred. R is aborting now ...
else 2L29: stop_on_error = if (is.numeric(options$error)) options$error else {eval(call) }, output_handler = knit_handlers(options$render, options))) if (options$error && options$include)
0L
else 2L30: }, output_handler = knit_handlers(options$render, options)))with_handlers({42: for (expr in tle$exprs) {eng_r(options)
ev <- withVisible(eval(expr, envir))
43: watcher$capture_plot_and_output()block_exec(params)42: watcher$print_value(ev$value, ev$visible, envir)
}eng_r(options)44: TRUEcall_block(x)
}, handlers)43:
block_exec(params)31: doWithOneRestart(return(expr), restart)
32: 45:
withOneRestart(expr, restarts[[1L]])process_group(group)44:
call_block(x)
33: 46: withRestartList(expr, restarts[-nr])
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 34: doWithOneRestart(return(expr), restart)45: error = function(e) {
if (progress && is.function(pb$interrupt)) 35: process_group(group) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
error <<- format(e)46:
})withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 36:
withRestartList(expr, restarts)47: error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) 37: if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({ pb$interrupt() pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())) watcher$print_value(ev$value, ev$visible, envir) }) }
TRUE48: 47: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { error = function(e) {38: if (progress && is.function(pb$interrupt)) evaluate::evaluate(...) pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check())
pb$interrupt() error <<- format(e)39: if (is_R_CMD_build() || is_R_CMD_check()) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error <<- format(e) }), list(rlang_trace_top_env = knit_global())) keep_message = if (is.numeric(options$message)) TRUE else options$message, }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd) write_utf8(res, output %n% stdout())48: stop_on_error = if (is.numeric(options$error)) options$error else {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) error = function(e) { if (options$error && options$include) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 0L
else 2L if (progress && is.function(pb$interrupt)) 49: }, output_handler = knit_handlers(options$render, options)) pb$interrupt()process_file(text, output)
if (is_R_CMD_build() || is_R_CMD_check())
40: error <<- format(e)in_dir(input_dir(), expr)50:
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)41:
write_utf8(res, output %n% stdout())in_input_dir(evaluate(code, envir = env, new_device = FALSE, paste0("\nQuitting from ", loc, if (!is.null(error)) 51: paste0("\n", rule(), error, "\n", rule()))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) output_dir = getwd(), ...) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {
49: 52: if (options$error && options$include) vweave_rmarkdown(...)process_file(text, output) 0L
53: 50: else 2Lknitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)engine$weave(file, quiet = quiet, encoding = enc)
54:
doTryCatch(return(expr), name, parentenv, handler) }, output_handler = knit_handlers(options$render, options)))
51: 55:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tryCatchOne(expr, names, parentenv, handlers[[1L]]) output_dir = getwd(), ...)42:
56: eng_r(options)tryCatchList(expr, classes, parentenv, handlers)
43: 52: 57: block_exec(params)tryCatch({vweave_rmarkdown(...)
engine$weave(file, quiet = quiet, encoding = enc)44:
setwd(startdir)call_block(x)
output <- find_vignette_product(name, by = "weave", engine = engine)53: 45: process_group(group) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)engine$weave(file, quiet = quiet, encoding = enc)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output <- find_vignette_product(name, by = "texi2pdf", error = function(e) {54: if (progress && is.function(pb$interrupt)) doTryCatch(return(expr), name, parentenv, handler) engine = engine) pb$interrupt()
}55: outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function(e) { error <<- format(e)
})56: thisOK <<- FALSE
fails <<- c(fails, file)tryCatchList(expr, classes, parentenv, handlers) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 47: file, conditionMessage(e)))
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 57: }) error = function(e) { if (progress && is.function(pb$interrupt))
tryCatch({58: pb$interrupt()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (is_R_CMD_build() || is_R_CMD_check()) engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWNAE3F/file839c28fbe291.rds") setwd(startdir) }), list(rlang_trace_top_env = knit_global()))
output <- find_vignette_product(name, by = "weave", engine = engine)An irrecoverable exception occurred. R is aborting now ...
if (!have.makefile && vignette_is_tex(output)) {48: texi2pdf(file = output, clean = FALSE, quiet = quiet)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output <- find_vignette_product(name, by = "texi2pdf", error = function(e) { engine = engine) if (progress && is.function(pb$interrupt)) } outputs <- c(outputs, output) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) { 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()))58: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWNAE3F/file839c28fbe291.rds")49:
process_file(text, output)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpWNAE3F/file839c28fbe291.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