Last updated on 2026-10-21 02:53:45 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.62 | 226.38 | 230.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.67 | 237.35 | 240.02 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 191.21 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 139.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.20 | 209.21 | 212.41 | 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 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 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 | 158.00 | 165.00 | 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
2026-10-21 08:04:48.195 R[42881:64976] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning")
Traceback:
*** caught segfault ***
1: address 0x110, cause 'invalid permissions'
RowCumsum(valid) }
}, error = function (cnd) 2: {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, watcher$capture_plot_and_output() tieBreak = FALSE, verbose = verbose) cnd <- sanitize_call(cnd)
watcher$push(cnd) 3: switch(on_error, continue = invokeRestart("eval_continue"), SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, stop = invokeRestart("eval_stop"), error = NULL) tau = tau, theta = th, exclusionRadius = exclusionRadius, }) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
28:
eval(call) 4:
ComputeError(predictions$Observations, predictions$Predictions)29:
eval(call) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 30: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, with_handlers({ embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) 6: watcher$capture_plot_and_output()FUN(X[[i]], ...) watcher$print_value(ev$value, ev$visible, envir)
} 7: TRUElapply(X = S, FUN = FUN, ...)}, handlers)
8:
doTryCatch(return(expr), name, parentenv, handler)31:
9: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: 10: withOneRestart(expr, restarts[[1L]])tryCatchList(expr, classes, parentenv, handlers)
33: 11: withRestartList(expr, restarts[-nr])tryCatch(expr, error = function(e) {
call <- conditionCall(e)34: if (!is.null(call)) {doWithOneRestart(return(expr), restart) if (identical(call[[1L]], quote(doTryCatch)))
35: call <- sys.call(-4L)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")36: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]withRestartList(expr, restarts) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 37: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], withRestarts(with_handlers({ type = "b") if (w > LONG) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) prefix <- paste0(prefix, "\n ") watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) } TRUE if (!silent && isTRUE(getOption("show.error.messages"))) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) cat(msg, file = outFile)
38: .Internal(printDeferredWarnings()) }evaluate::evaluate(...) invisible(structure(msg, class = "try-error", condition = e))
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, 12: stop_on_error = if (is.numeric(options$error)) options$error else {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (options$error && options$include)
0L13: else 2LsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }, output_handler = knit_handlers(options$render, options))
14: FUN(X[[i]], ...)40:
in_dir(input_dir(), expr)15:
lapply(seq_len(cores), inner.do)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 17: stop_on_error = if (is.numeric(options$error)) options$error else {doTryCatch(return(expr), name, parentenv, handler) if (options$error && options$include) 0L else 2L
}, output_handler = knit_handlers(options$render, options)))18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])42:
eng_r(options)19:
tryCatchList(expr, classes, parentenv, handlers)43:
block_exec(params)
Traceback:
20: 1: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)RowCumsum(valid)44:
call_block(x) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 45: process_group(group)21:
46: tieBreak = FALSE, verbose = verbose)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), SweepApply(theta, worker, numProcess)
error = function(e) { 3:
if (progress && is.function(pb$interrupt)) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, pb$interrupt() tau = tau, theta = th, exclusionRadius = exclusionRadius, 22: if (is_R_CMD_build() || is_R_CMD_check()) unlist(SweepApply(theta, worker, numProcess)) embedded = embedded, validLib = validLib, noTime = noTime, error <<- format(e) })
ignoreNan = ignoreNan, backend = backend)47:
23: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 4: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) error = function(e) {
if (progress && is.function(pb$interrupt)) 24: ComputeError(predictions$Observations, predictions$Predictions)eval(expr, envir)
pb$interrupt()25: 5: if (is_R_CMD_build() || is_R_CMD_check()) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, error <<- format(e) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, eval(expr, envir) }), list(rlang_trace_top_env = knit_global())) embedded = embedded, validLib = validLib, noTime = noTime,
26:
ignoreNan = ignoreNan, backend = backend)$predictions)48: withVisible(eval(expr, envir))
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 6: FUN(X[[i]], ...)27: error = function(e) {withCallingHandlers(code, error = function (e)
if (progress && is.function(pb$interrupt)) 7: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) lapply(X = S, FUN = FUN, ...) error <<- format(e)
rlang::entrace(e), message = function (cnd) }), list(rlang_trace_top_env = knit_global())), function(loc) { 8: setwd(wd)doTryCatch(return(expr), name, parentenv, handler) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) { 9: paste0("\n", rule(), error, "\n", rule())) watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]])}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
if (on_message$capture) {10:
watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers)49:
}process_file(text, output) if (on_message$silence) {
11: 50: invokeRestart("muffleMessage")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)tryCatch(expr, error = function(e) { } call <- conditionCall(e)
if (!is.null(call)) {51: }, warning = function (cnd) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) if (identical(call[[1L]], quote(doTryCatch)))
{52: call <- sys.call(-4L) if (getOption("warn") >= 2 || getOption("warn") < 0) { dcall <- deparse(call, nlines = 1L) return() prefix <- paste("Error in", dcall, ": ")vweave_rmarkdown(...) LONG <- 75L }
sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$capture_plot_and_output()53: if (on_warning$capture) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cnd <- sanitize_call(cnd)engine$weave(file, quiet = quiet, encoding = enc) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$push(cnd)54: }doTryCatch(return(expr), name, parentenv, handler) type = "b") if (on_warning$silence) { if (w > LONG)
invokeRestart("muffleWarning")55: prefix <- paste0(prefix, "\n ")tryCatchOne(expr, names, parentenv, handlers[[1L]]) }}, error = function (cnd) { watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd)
else prefix <- "Error : " watcher$push(cnd)56: switch(on_error, continue = invokeRestart("eval_continue"), msg <- paste0(prefix, conditionMessage(e), "\n") stop = invokeRestart("eval_stop"), error = NULL)tryCatchList(expr, classes, parentenv, handlers)})
.Internal(seterrmessage(msg[1L]))57:
tryCatch({ if (!silent && isTRUE(getOption("show.error.messages"))) {28: cat(msg, file = outFile) engine$weave(file, quiet = quiet, encoding = enc)eval(call) setwd(startdir) .Internal(printDeferredWarnings()) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { } texi2pdf(file = output, clean = FALSE, quiet = quiet)29: output <- find_vignette_product(name, by = "texi2pdf", eval(call) invisible(structure(msg, class = "try-error", condition = e))
engine = engine)}) }30: outputs <- c(outputs, output)with_handlers({}, error = function(e) {
thisOK <<- FALSE12: for (expr in tle$exprs) { fails <<- c(fails, file) ev <- withVisible(eval(expr, envir))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", watcher$capture_plot_and_output() file, conditionMessage(e)))
}) watcher$print_value(ev$value, ev$visible, envir)
}13: 58: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
TRUE skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEcbBD7/file879d7761c95b.rds")14:
}, handlers)An irrecoverable exception occurred. R is aborting now ...
FUN(X[[i]], ...)
31: 15: doWithOneRestart(return(expr), restart)
Traceback:
lapply(seq_len(cores), inner.do)
32: 1: withOneRestart(expr, restarts[[1L]])RowCumsum(valid)
33: withRestartList(expr, restarts[-nr]) 2:
16: 34: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, doWithOneRestart(return(expr), restart)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) tieBreak = FALSE, verbose = verbose)17:
36: doTryCatch(return(expr), name, parentenv, handler)withRestartList(expr, restarts)
3: 37: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, withRestarts(with_handlers({
for (expr in tle$exprs) { tau = tau, theta = th, exclusionRadius = exclusionRadius, ev <- withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime, 18: ignoreNan = ignoreNan, backend = backend) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4:
}19: ComputeError(predictions$Observations, predictions$Predictions) TRUE
tryCatchList(expr, classes, parentenv, handlers) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 20: embedded = embedded, validLib = validLib, noTime = noTime, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, ignoreNan = ignoreNan, backend = backend)$predictions) mc.preschedule = TRUE), error = function(e) NULL)
6: 21: FUN(X[[i]], ...)SweepApply(theta, worker, numProcess)
7: 22: lapply(X = S, FUN = FUN, ...)unlist(SweepApply(theta, worker, numProcess))
8: 23: doTryCatch(return(expr), name, parentenv, handler)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) E = E, showPlot = TRUE)
38: 24: 9: eval(expr, envir)evaluate::evaluate(...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: 25: 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 11: stop_on_error = if (is.numeric(options$error)) options$error else {tryCatch(expr, error = function(e) { if (options$error && options$include) call <- conditionCall(e)
if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 26: 0L call <- sys.call(-4L) else 2L dcall <- deparse(call, nlines = 1L) }, output_handler = knit_handlers(options$render, options))withVisible(eval(expr, envir)) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]27: 40: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")in_dir(input_dir(), expr)
if (is.na(w)) withCallingHandlers(code, error = function (e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], rlang::entrace(e), message = function (cnd) 41: {in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$capture_plot_and_output() keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, type = "b") if (on_message$capture) { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { if (w > LONG) if (options$error && options$include) } 0L prefix <- paste0(prefix, "\n ") if (on_message$silence) { else 2L } }, output_handler = knit_handlers(options$render, options))) invokeRestart("muffleMessage") else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")
}, warning = function (cnd) .Internal(seterrmessage(msg[1L])){ if (!silent && isTRUE(getOption("show.error.messages"))) { if (getOption("warn") >= 2 || getOption("warn") < 0) {42: cat(msg, file = outFile) return()eng_r(options) .Internal(printDeferredWarnings()) } } watcher$capture_plot_and_output()
if (on_warning$capture) {43: cnd <- sanitize_call(cnd)block_exec(params) invisible(structure(msg, class = "try-error", condition = e))
44: watcher$push(cnd)call_block(x)}) }
12: if (on_warning$silence) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)45: invokeRestart("muffleWarning")process_group(group) }
46: 13: }, error = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (progress && is.function(pb$interrupt))
watcher$capture_plot_and_output() pb$interrupt() cnd <- sanitize_call(cnd) if (is_R_CMD_build() || is_R_CMD_check()) 14: watcher$push(cnd) error <<- format(e) switch(on_error, continue = invokeRestart("eval_continue"), FUN(X[[i]], ...) })
15:
stop = invokeRestart("eval_stop"), error = NULL)47: })lapply(seq_len(cores), inner.do)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
if (progress && is.function(pb$interrupt)) 28: 16: eval(call) pb$interrupt()
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (is_R_CMD_build() || is_R_CMD_check()) 29: error <<- format(e)eval(call)
}), list(rlang_trace_top_env = knit_global()))30: 17:
with_handlers({doTryCatch(return(expr), name, parentenv, handler) for (expr in tle$exprs) {48:
ev <- withVisible(eval(expr, envir))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 18: watcher$capture_plot_and_output() error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir) if (progress && is.function(pb$interrupt))
}19: pb$interrupt()tryCatchList(expr, classes, parentenv, handlers) if (is_R_CMD_build() || is_R_CMD_check())
TRUE error <<- format(e)}, handlers)20: }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)31: write_utf8(res, output %n% stdout())doWithOneRestart(return(expr), restart)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL) paste0("\nQuitting from ", loc, if (!is.null(error)) 32:
paste0("\n", rule(), error, "\n", rule()))21: withOneRestart(expr, restarts[[1L]])}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)SweepApply(theta, worker, numProcess)
49:
33: 22: process_file(text, output)unlist(SweepApply(theta, worker, numProcess))withRestartList(expr, restarts[-nr])
23:
34: 50: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", doWithOneRestart(return(expr), restart) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) E = E, showPlot = TRUE)
51: 24: 35: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) output_dir = getwd(), ...)
eval(expr, envir)36:
withRestartList(expr, restarts)52: 25:
vweave_rmarkdown(...)37: eval(expr, envir)
withRestarts(with_handlers({
53: for (expr in tle$exprs) {26: engine$weave(file, quiet = quiet, encoding = enc) ev <- withVisible(eval(expr, envir))
withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
54: watcher$print_value(ev$value, ev$visible, envir)doTryCatch(return(expr), name, parentenv, handler)27:
withCallingHandlers(code, error = function (e) }55: rlang::entrace(e), message = function (cnd) TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]]){}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
watcher$capture_plot_and_output()
if (on_message$capture) {56: 38: watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) }evaluate::evaluate(...)
57: 39: if (on_message$silence) {tryCatch({evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleMessage") engine$weave(file, quiet = quiet, encoding = enc) keep_message = if (is.numeric(options$message)) TRUE else options$message, } setwd(startdir) stop_on_error = if (is.numeric(options$error)) options$error else {}, warning = function (cnd) output <- find_vignette_product(name, by = "weave", engine = engine) if (options$error && options$include) { if (!have.makefile && vignette_is_tex(output)) { 0L if (getOption("warn") >= 2 || getOption("warn") < 0) { else 2L texi2pdf(file = output, clean = FALSE, quiet = quiet) }, output_handler = knit_handlers(options$render, options)) return() output <- find_vignette_product(name, by = "texi2pdf",
}40: watcher$capture_plot_and_output() engine = engine) if (on_warning$capture) {in_dir(input_dir(), expr) } cnd <- sanitize_call(cnd)
watcher$push(cnd)41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_warning$silence) { keep_message = if (is.numeric(options$message)) TRUE else options$message, outputs <- c(outputs, output) invokeRestart("muffleWarning")}, error = function(e) { } stop_on_error = if (is.numeric(options$error)) options$error else {}, error = function (cnd) if (options$error && options$include) thisOK <<- FALSE{ fails <<- c(fails, file) 0L message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", watcher$capture_plot_and_output() file, conditionMessage(e))) else 2L cnd <- sanitize_call(cnd)}) watcher$push(cnd)
}, output_handler = knit_handlers(options$render, options))) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)58: })tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 42: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEcbBD7/file879d7761c95b.rds")eng_r(options)
28:
43: An irrecoverable exception occurred. R is aborting now ...
eval(call)block_exec(params)
44: 29: call_block(x)eval(call)
45:
process_group(group)30:
with_handlers({46: for (expr in tle$exprs) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ev <- withVisible(eval(expr, envir)) error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) watcher$print_value(ev$value, ev$visible, envir) pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) TRUE error <<- format(e)}, handlers)
})31:
doWithOneRestart(return(expr), restart)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 32: error = function(e) { if (progress && is.function(pb$interrupt)) withOneRestart(expr, restarts[[1L]]) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 33: withRestartList(expr, restarts[-nr]) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))34:
doWithOneRestart(return(expr), restart)48:
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
36: error = function(e) {withRestartList(expr, restarts)
if (progress && is.function(pb$interrupt)) 37: pb$interrupt()withRestarts(with_handlers({ for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$capture_plot_and_output() setwd(wd) watcher$print_value(ev$value, ev$visible, envir) } write_utf8(res, output %n% stdout()) TRUE paste0("\nQuitting from ", loc, if (!is.null(error)) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
38: 49: evaluate::evaluate(...)process_file(text, output)
39: 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)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, 51: stop_on_error = if (is.numeric(options$error)) options$error else {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (options$error && options$include) output_dir = getwd(), ...) 0L
else 2L52: }, output_handler = knit_handlers(options$render, options))vweave_rmarkdown(...)
40: 53: in_dir(input_dir(), expr)engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
55: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchOne(expr, names, parentenv, handlers[[1L]]) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 56: tryCatchList(expr, classes, parentenv, handlers)
0L57: else 2LtryCatch({ }, output_handler = knit_handlers(options$render, options))) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)42: output <- find_vignette_product(name, by = "weave", engine = engine)eng_r(options) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)43: output <- find_vignette_product(name, by = "texi2pdf", block_exec(params) engine = engine)
}44: outputs <- c(outputs, output)call_block(x)}, error = function(e) {
thisOK <<- FALSE45: fails <<- c(fails, file)process_group(group) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))46: })withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {58: if (progress && is.function(pb$interrupt)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt() skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEcbBD7/file879d7761c95b.rds")
if (is_R_CMD_build() || is_R_CMD_check()) An irrecoverable exception occurred. R is aborting now ...
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/RtmpEcbBD7/file879d7761c95b.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