Last updated on 2026-10-29 15:54:55 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.97 | 226.48 | 230.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.50 | 235.90 | 238.40 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.82 | 207.25 | 211.07 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.10 | 211.40 | 214.50 | 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 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 46.00 | 48.00 | 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 | 161.00 | 169.00 | 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
2026-10-29 20:46:15.304 R[53383:80126] 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:
Traceback:
1: tryCatch(expr, error = function(e) {RowCumsum(valid) call <- conditionCall(e)
2: if (!is.null(call)) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (identical(call[[1L]], quote(doTryCatch))) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) call <- sys.call(-4L)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, dcall <- deparse(call, nlines = 1L) tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, prefix <- paste("Error in", dcall, ": ") ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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)
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], 6: type = "b")FUN(X[[i]], ...)
if (w > LONG) 7: lapply(X = S, FUN = FUN, ...)
prefix <- paste0(prefix, "\n ") 8: doTryCatch(return(expr), name, parentenv, handler) }
else prefix <- "Error : " 9: msg <- paste0(prefix, conditionMessage(e), "\n")tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
10: cat(msg, file = outFile)tryCatchList(expr, classes, parentenv, handlers) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition = e))})
11: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (identical(call[[1L]], quote(doTryCatch)))
14: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)FUN(X[[i]], ...) prefix <- paste("Error in", dcall, ": ")
15: LONG <- 75Llapply(seq_len(cores), inner.do) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")16: if (is.na(w)) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")17: if (w > LONG) doTryCatch(return(expr), name, parentenv, handler) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : "18: msg <- paste0(prefix, conditionMessage(e), "\n")tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {19: cat(msg, file = outFile)tryCatchList(expr, classes, parentenv, handlers) .Internal(printDeferredWarnings())
}20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, invisible(structure(msg, class = "try-error", condition = e)) mc.preschedule = TRUE), error = function(e) NULL)})
21: SweepApply(theta, worker, numProcess)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
22: unlist(SweepApply(theta, worker, numProcess))13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
23:
14: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)24: eval(expr, envir)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)25:
eval(expr, envir)17:
doTryCatch(return(expr), name, parentenv, handler)26:
withVisible(eval(expr, envir))18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])27:
withCallingHandlers(code, error = function (e) 19: rlang::entrace(e), message = function (cnd) tryCatchList(expr, classes, parentenv, handlers){
watcher$capture_plot_and_output()20: if (on_message$capture) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$push(cnd) mc.preschedule = TRUE), error = function(e) NULL) }
if (on_message$silence) {21: invokeRestart("muffleMessage")SweepApply(theta, worker, numProcess) }}, warning = function (cnd)
{22: if (getOption("warn") >= 2 || getOption("warn") < 0) {unlist(SweepApply(theta, worker, numProcess)) return()
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
}24: watcher$capture_plot_and_output()eval(expr, envir) if (on_warning$capture) {
cnd <- sanitize_call(cnd) watcher$push(cnd)25: }eval(expr, envir) if (on_warning$silence) {
invokeRestart("muffleWarning") }26: }, error = function (cnd) {withVisible(eval(expr, envir))
watcher$capture_plot_and_output()27: cnd <- sanitize_call(cnd)withCallingHandlers(code, error = function (e) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) {})
watcher$push(cnd)28: }eval(call) if (on_message$silence) {
invokeRestart("muffleMessage")29: }eval(call)
}, warning = function (cnd) 30: with_handlers({ for (expr in tle$exprs) {{ ev <- withVisible(eval(expr, envir)) if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$capture_plot_and_output() return() } watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() } if (on_warning$capture) { TRUE}, handlers) cnd <- sanitize_call(cnd)
31: doWithOneRestart(return(expr), restart)
watcher$push(cnd)32: withOneRestart(expr, restarts[[1L]])
}
Traceback:
1: 33: RowCumsum(valid)
withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart) if (on_warning$silence) {
invokeRestart("muffleWarning") }35: }, error = function (cnd) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]){ watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)36: watcher$push(cnd)withRestartList(expr, restarts) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)37: })withRestarts(with_handlers({ for (expr in tle$exprs) {
2: 28: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, eval(call)
Traceback:
validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)29: 1:
eval(call)RowCumsum(valid)
3: 30:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 2: with_handlers({ tau = tau, theta = th, exclusionRadius = exclusionRadius, for (expr in tle$exprs) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ev <- withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() ignoreNan = ignoreNan, backend = backend) watcher$capture_plot_and_output() tieBreak = FALSE, verbose = verbose) watcher$print_value(ev$value, ev$visible, envir)
watcher$print_value(ev$value, ev$visible, envir) 4: } 3: }ComputeError(predictions$Observations, predictions$Predictions)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, TRUE TRUE tau = tau, theta = th, exclusionRadius = exclusionRadius, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)}, handlers) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)38:
31: evaluate::evaluate(...)
doWithOneRestart(return(expr), restart) 4:
ComputeError(predictions$Observations, predictions$Predictions) 5:
39:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 32: 5: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, withOneRestart(expr, restarts[[1L]]) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, keep_message = if (is.numeric(options$message)) TRUE else options$message,
embedded = embedded, validLib = validLib, noTime = noTime, embedded = embedded, validLib = validLib, noTime = noTime, stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend)$predictions)33: ignoreNan = ignoreNan, backend = backend)$predictions)withRestartList(expr, restarts[-nr]) if (options$error && options$include)
34: 6: 0LdoWithOneRestart(return(expr), restart) 6: FUN(X[[i]], ...) else 2L
FUN(X[[i]], ...) 7: }, output_handler = knit_handlers(options$render, options))lapply(X = S, FUN = FUN, ...)35:
8: 7: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])doTryCatch(return(expr), name, parentenv, handler)lapply(X = S, FUN = FUN, ...)
8: 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
36:
withRestartList(expr, restarts)10: 9: tryCatchList(expr, classes, parentenv, handlers)
tryCatchOne(expr, names, parentenv, handlers[[1L]])11: tryCatch(expr, error = function(e) {40:
37: call <- conditionCall(e)withRestarts(with_handlers({ if (!is.null(call)) {in_dir(input_dir(), expr) if (identical(call[[1L]], quote(doTryCatch))) 10: for (expr in tle$exprs) { call <- sys.call(-4L)
tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L) ev <- withVisible(eval(expr, envir)) prefix <- paste("Error in", dcall, ": ")
41: LONG <- 75L watcher$capture_plot_and_output()11: in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$print_value(ev$value, ev$visible, envir) sm <- strsplit(conditionMessage(e), "\n")[[1L]] }tryCatch(expr, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") TRUE keep_message = if (is.numeric(options$message)) TRUE else options$message, call <- conditionCall(e) stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (options$error && options$include) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
if (!is.null(call)) { 0L type = "b")38: evaluate::evaluate(...) if (w > LONG)
if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste0(prefix, "\n ") else 2L39: }, output_handler = knit_handlers(options$render, options))) call <- sys.call(-4L) }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, .Internal(seterrmessage(msg[1L]))42: dcall <- deparse(call, nlines = 1L) keep_message = if (is.numeric(options$message)) TRUE else options$message, prefix <- paste("Error in", dcall, ": ")eng_r(options) if (!silent && isTRUE(getOption("show.error.messages"))) {
stop_on_error = if (is.numeric(options$error)) options$error else {43: LONG <- 75L if (options$error && options$include) block_exec(params) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 0L
cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")44: .Internal(printDeferredWarnings()) else 2L if (is.na(w)) call_block(x) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, output_handler = knit_handlers(options$render, options)) }
type = "b") invisible(structure(msg, class = "try-error", condition = e))40: 45: if (w > LONG) process_group(group)})in_dir(input_dir(), expr)
prefix <- paste0(prefix, "\n ")
41: }46: else prefix <- "Error : "in_input_dir(evaluate(code, envir = env, new_device = FALSE, msg <- paste0(prefix, conditionMessage(e), "\n") keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 12: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), .Internal(seterrmessage(msg[1L]))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (!silent && isTRUE(getOption("show.error.messages"))) { error = function(e) { cat(msg, file = outFile) keep_message = if (is.numeric(options$message)) TRUE else options$message, .Internal(printDeferredWarnings())
stop_on_error = if (is.numeric(options$error)) options$error else { if (progress && is.function(pb$interrupt)) } if (options$error && options$include) invisible(structure(msg, class = "try-error", condition = e)) pb$interrupt()13: 0L}) if (is_R_CMD_build() || is_R_CMD_check()) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else 2L
}, output_handler = knit_handlers(options$render, options)))14: 12: error <<- format(e)
FUN(X[[i]], ...) })
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)47: 42:
eng_r(options)15: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
13: error = function(e) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))lapply(seq_len(cores), inner.do)43: if (progress && is.function(pb$interrupt))
block_exec(params) pb$interrupt()14:
FUN(X[[i]], ...) if (is_R_CMD_build() || is_R_CMD_check()) 16: error <<- format(e)44: call_block(x)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)15: }), list(rlang_trace_top_env = knit_global()))
lapply(seq_len(cores), inner.do)
45:
17: process_group(group)
48: 46: doTryCatch(return(expr), name, parentenv, handler)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) pb$interrupt()18: error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (progress && is.function(pb$interrupt)) 17: }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt()doTryCatch(return(expr), name, parentenv, handler)19:
tryCatchList(expr, classes, parentenv, handlers)
setwd(wd) if (is_R_CMD_build() || is_R_CMD_check()) 20: 18: write_utf8(res, output %n% stdout()) error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) })
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 19:
paste0("\nQuitting from ", loc, if (!is.null(error)) mc.preschedule = TRUE), error = function(e) NULL)47: tryCatchList(expr, classes, parentenv, handlers) paste0("\n", rule(), error, "\n", rule()))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
20: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)21: error = function(e) {tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SweepApply(theta, worker, numProcess)
mc.preschedule = TRUE), error = function(e) NULL) if (progress && is.function(pb$interrupt))
49: pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 22: process_file(text, output)21:
error <<- format(e)SweepApply(theta, worker, numProcess)unlist(SweepApply(theta, worker, numProcess))50:
}), list(rlang_trace_top_env = knit_global()))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)22:
unlist(SweepApply(theta, worker, numProcess))48:
51: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 23: 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), error = function(e) {PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (progress && is.function(pb$interrupt)) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", output_dir = getwd(), ...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 52: E = E, showPlot = TRUE) error <<- format(e)vweave_rmarkdown(...)
}), list(rlang_trace_top_env = knit_global())), function(loc) { E = E, showPlot = TRUE)
24:
53: 24: eval(expr, envir) setwd(wd)engine$weave(file, quiet = quiet, encoding = enc) write_utf8(res, output %n% stdout())eval(expr, envir)
54: 25: paste0("\nQuitting from ", loc, if (!is.null(error)) 25: paste0("\n", rule(), error, "\n", rule()))eval(expr, envir)doTryCatch(return(expr), name, parentenv, handler)eval(expr, envir)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)26: 26:
withVisible(eval(expr, envir))
withVisible(eval(expr, envir))
49: 27:
withCallingHandlers(code, error = function (e) 27: 55: rlang::entrace(e), message = function (cnd) process_file(text, output){
tryCatchOne(expr, names, parentenv, handlers[[1L]])withCallingHandlers(code, error = function (e) watcher$capture_plot_and_output()rlang::entrace(e), message = function (cnd)
if (on_message$capture) {56: {tryCatchList(expr, classes, parentenv, handlers) watcher$push(cnd)
watcher$capture_plot_and_output() }50: 57: if (on_message$capture) { if (on_message$silence) { watcher$push(cnd)tryCatch({knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
invokeRestart("muffleMessage")51: engine$weave(file, quiet = quiet, encoding = enc)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), setwd(startdir) if (on_message$silence) { } output_dir = getwd(), ...) output <- find_vignette_product(name, by = "weave", engine = engine)}, warning = function (cnd)
invokeRestart("muffleMessage"){ } if (!have.makefile && vignette_is_tex(output)) { if (getOption("warn") >= 2 || getOption("warn") < 0) { texi2pdf(file = output, clean = FALSE, quiet = quiet) return()}, warning = function (cnd) 52: output <- find_vignette_product(name, by = "texi2pdf", { }vweave_rmarkdown(...) engine = engine) watcher$capture_plot_and_output() if (on_warning$capture) { if (getOption("warn") >= 2 || getOption("warn") < 0) {
cnd <- sanitize_call(cnd) return() watcher$push(cnd) }53: }engine$weave(file, quiet = quiet, encoding = enc) } outputs <- c(outputs, output) if (on_warning$silence) {
watcher$capture_plot_and_output()54: if (on_warning$capture) { cnd <- sanitize_call(cnd) invokeRestart("muffleWarning")doTryCatch(return(expr), name, parentenv, handler)}, error = function(e) { } watcher$push(cnd)}, error = function (cnd)
thisOK <<- FALSE{55: fails <<- c(fails, file) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", watcher$capture_plot_and_output() if (on_warning$silence) { cnd <- sanitize_call(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) invokeRestart("muffleWarning") }
file, conditionMessage(e))) watcher$push(cnd)}, error = function (cnd) 56: }) switch(on_error, continue = invokeRestart("eval_continue"), {tryCatchList(expr, classes, parentenv, handlers) stop = invokeRestart("eval_stop"), error = NULL) watcher$capture_plot_and_output()})
cnd <- sanitize_call(cnd)57: 58: 28: tryCatch({ watcher$push(cnd)eval(call)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEiogX1/file909a55cafed2.rds")
engine$weave(file, quiet = quiet, encoding = enc)
29: An irrecoverable exception occurred. R is aborting now ...
eval(call)}) setwd(startdir)
30: output <- find_vignette_product(name, by = "weave", engine = engine)with_handlers({28: if (!have.makefile && vignette_is_tex(output)) { for (expr in tle$exprs) {eval(call) ev <- withVisible(eval(expr, envir))
texi2pdf(file = output, clean = FALSE, quiet = quiet)29: output <- find_vignette_product(name, by = "texi2pdf", eval(call) engine = engine) watcher$capture_plot_and_output() }
outputs <- c(outputs, output)30: watcher$print_value(ev$value, ev$visible, envir)with_handlers({ } for (expr in tle$exprs) { TRUE}, error = function(e) {}, handlers) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
thisOK <<- FALSE watcher$print_value(ev$value, ev$visible, envir)31: }doWithOneRestart(return(expr), restart) fails <<- c(fails, file) TRUE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
32: 58: }, handlers)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
withOneRestart(expr, restarts[[1L]])31:
doWithOneRestart(return(expr), restart) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEiogX1/file909a55cafed2.rds")33:
withRestartList(expr, restarts[-nr])
An irrecoverable exception occurred. R is aborting now ...
32: 34: withOneRestart(expr, restarts[[1L]])doWithOneRestart(return(expr), restart)
33: 35: withRestartList(expr, restarts[-nr])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36:
withRestartList(expr, restarts)34:
doWithOneRestart(return(expr), restart)37:
withRestarts(with_handlers({35: for (expr in tle$exprs) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)36: }withRestartList(expr, restarts) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)37:
38: withRestarts(with_handlers({evaluate::evaluate(...) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$print_value(ev$value, ev$visible, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (options$error && options$include)
0L38: else 2Levaluate::evaluate(...)
}, output_handler = knit_handlers(options$render, options))39:
40: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, in_dir(input_dir(), expr) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0L41: else 2Lin_input_dir(evaluate(code, envir = env, new_device = FALSE, }, output_handler = knit_handlers(options$render, options))
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 40: in_dir(input_dir(), expr) keep_message = if (is.numeric(options$message)) TRUE else options$message,
41: stop_on_error = if (is.numeric(options$error)) options$error else {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (options$error && options$include) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) else 2L 0L else 2L }, output_handler = knit_handlers(options$render, options))) }, output_handler = knit_handlers(options$render, options)))
42:
42: eng_r(options)eng_r(options)
43: 43: block_exec(params)block_exec(params)
44: 44: call_block(x)call_block(x)
45: 45: process_group(group)process_group(group)
46:
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(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) { })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) pb$interrupt() error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: }), list(rlang_trace_top_env = knit_global()))xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {48: if (progress && is.function(pb$interrupt)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { error = function(e) { setwd(wd) if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) pb$interrupt() paste0("\nQuitting from ", loc, if (!is.null(error)) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) paste0("\n", rule(), error, "\n", rule())) }), list(rlang_trace_top_env = knit_global())), function(loc) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) setwd(wd)
write_utf8(res, output %n% stdout())49: paste0("\nQuitting from ", loc, if (!is.null(error)) process_file(text, output)
paste0("\n", rule(), error, "\n", rule()))50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: 51: process_file(text, output)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
50: 52: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
vweave_rmarkdown(...)
51: 53: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), engine$weave(file, quiet = quiet, encoding = enc)
output_dir = getwd(), ...)54:
52: doTryCatch(return(expr), name, parentenv, handler)
vweave_rmarkdown(...)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: 53: tryCatchList(expr, classes, parentenv, handlers)
engine$weave(file, quiet = quiet, encoding = enc)57:
tryCatch({54: doTryCatch(return(expr), name, parentenv, handler) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
55: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)56: output <- find_vignette_product(name, by = "texi2pdf", tryCatchList(expr, classes, parentenv, handlers) engine = engine)
}57: outputs <- c(outputs, output)tryCatch({}, error = function(e) { engine$weave(file, quiet = quiet, encoding = enc) thisOK <<- FALSE setwd(startdir) fails <<- c(fails, file) output <- find_vignette_product(name, by = "weave", engine = engine) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (!have.makefile && vignette_is_tex(output)) { file, conditionMessage(e))) texi2pdf(file = output, clean = FALSE, quiet = quiet)}) output <- find_vignette_product(name, by = "texi2pdf",
58: engine = engine)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpEiogX1/file909a55cafed2.rds") outputs <- c(outputs, output)
}, error = function(e) {An irrecoverable exception occurred. R is aborting now ...
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/RtmpEiogX1/file909a55cafed2.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