Last updated on 2026-10-21 05:56:52 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 | 2.00 | 37.00 | 39.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 159.00 | 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 15:31:03.940 R[45526:67832] 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:
Traceback:
FUN(X[[i]], ...) 1: RowCumsum(valid)
15: 2: lapply(seq_len(cores), inner.do)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
17: 3: doTryCatch(return(expr), name, parentenv, handler)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 18: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: 19: ComputeError(predictions$Observations, predictions$Predictions)
tryCatchList(expr, classes, parentenv, handlers) 5:
20: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, mc.preschedule = TRUE), error = function(e) NULL) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)21:
SweepApply(theta, worker, numProcess)
6: 22: FUN(X[[i]], ...)unlist(SweepApply(theta, worker, numProcess))
7: 23: lapply(X = S, FUN = FUN, ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 8:
doTryCatch(return(expr), name, parentenv, handler)24:
9: eval(expr, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 25: tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
11: 26: tryCatch(expr, error = function(e) {withVisible(eval(expr, envir)) call <- conditionCall(e)
if (!is.null(call)) {27: if (identical(call[[1L]], quote(doTryCatch))) withCallingHandlers(code, error = function (e) call <- sys.call(-4L)rlang::entrace(e), message = function (cnd) dcall <- deparse(call, nlines = 1L){ prefix <- paste("Error in", dcall, ": ") watcher$capture_plot_and_output() LONG <- 75L if (on_message$capture) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$push(cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) if (on_message$silence) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invokeRestart("muffleMessage") type = "b") } if (w > LONG) }, warning = function (cnd) prefix <- paste0(prefix, "\n "){ } if (getOption("warn") >= 2 || getOption("warn") < 0) { else prefix <- "Error : " return() msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) watcher$capture_plot_and_output() if (on_warning$capture) { if (!silent && isTRUE(getOption("show.error.messages"))) { cnd <- sanitize_call(cnd) cat(msg, file = outFile) watcher$push(cnd) .Internal(printDeferredWarnings()) } } if (on_warning$silence) { invisible(structure(msg, class = "try-error", condition = e)) invokeRestart("muffleWarning")}) }
}, error = function (cnd) 12: { watcher$capture_plot_and_output()try(lapply(X = S, FUN = FUN, ...), silent = TRUE) cnd <- sanitize_call(cnd)
watcher$push(cnd)13: switch(on_error, continue = invokeRestart("eval_continue"), sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) stop = invokeRestart("eval_stop"), error = NULL)
})
14:
Traceback:
FUN(X[[i]], ...)28: eval(call)
1:
15: 29: RowCumsum(valid)lapply(seq_len(cores), inner.do)
2: 16: eval(call)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
30: tieBreak = FALSE, verbose = verbose)17:
doTryCatch(return(expr), name, parentenv, handler)with_handlers({
for (expr in tle$exprs) { 3: 18: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ev <- withVisible(eval(expr, envir)) tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) embedded = embedded, validLib = validLib, noTime = noTime, watcher$capture_plot_and_output() ignoreNan = ignoreNan, backend = backend)
watcher$print_value(ev$value, ev$visible, envir) 4: }19: ComputeError(predictions$Observations, predictions$Predictions) TRUEtryCatchList(expr, classes, parentenv, handlers)
}, handlers)
5:
20: 31: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, doWithOneRestart(return(expr), restart) mc.preschedule = TRUE), error = function(e) NULL)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,
21: 32: ignoreNan = ignoreNan, backend = backend)$predictions)SweepApply(theta, worker, numProcess)
withOneRestart(expr, restarts[[1L]])22:
6: unlist(SweepApply(theta, worker, numProcess))FUN(X[[i]], ...)
23: 33: 7: withRestartList(expr, restarts[-nr])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", lapply(X = S, FUN = FUN, ...)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 34: 8: doWithOneRestart(return(expr), restart) E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler)
35: 9:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatchOne(expr, names, parentenv, handlers[[1L]])24:
36: eval(expr, envir)10: withRestartList(expr, restarts)
37: 25: withRestarts(with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {eval(expr, envir) ev <- withVisible(eval(expr, envir))
26: watcher$capture_plot_and_output()11: watcher$print_value(ev$value, ev$visible, envir)withVisible(eval(expr, envir)) }tryCatch(expr, error = function(e) {
TRUE27: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
withCallingHandlers(code, error = function (e) 38: rlang::entrace(e), message = function (cnd) call <- conditionCall(e){evaluate::evaluate(...) if (!is.null(call)) {
watcher$capture_plot_and_output() if (identical(call[[1L]], quote(doTryCatch))) 39: if (on_message$capture) { call <- sys.call(-4L) watcher$push(cnd) dcall <- deparse(call, nlines = 1L) }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, prefix <- paste("Error in", dcall, ": ") keep_message = if (is.numeric(options$message)) TRUE else options$message, if (on_message$silence) { stop_on_error = if (is.numeric(options$error)) options$error else { invokeRestart("muffleMessage") if (options$error && options$include) } 0L LONG <- 75L else 2L}, warning = function (cnd) }, output_handler = knit_handlers(options$render, options)){ sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (getOption("warn") >= 2 || getOption("warn") < 0) {40: return() if (is.na(w)) }in_dir(input_dir(), expr) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
watcher$capture_plot_and_output()41: if (on_warning$capture) { type = "b")in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (w > LONG) cnd <- sanitize_call(cnd) prefix <- paste0(prefix, "\n ") keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd) } keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { if (on_warning$silence) { else prefix <- "Error : " invokeRestart("muffleWarning") if (options$error && options$include) } msg <- paste0(prefix, conditionMessage(e), "\n") 0L .Internal(seterrmessage(msg[1L]))}, error = function (cnd) if (!silent && isTRUE(getOption("show.error.messages"))) { else 2L cat(msg, file = outFile) }, output_handler = knit_handlers(options$render, options))){
watcher$capture_plot_and_output()42: cnd <- sanitize_call(cnd)eng_r(options) .Internal(printDeferredWarnings())
watcher$push(cnd)43: }block_exec(params) switch(on_error, continue = invokeRestart("eval_continue"), invisible(structure(msg, class = "try-error", condition = e)) stop = invokeRestart("eval_stop"), error = NULL)})})
12: 44: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
call_block(x)13: 28:
eval(call)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
45:
29: process_group(group)eval(call)
14: 46:
FUN(X[[i]], ...)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
30: 15: error = function(e) {lapply(seq_len(cores), inner.do)with_handlers({
if (progress && is.function(pb$interrupt)) 16: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) pb$interrupt()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check())
watcher$print_value(ev$value, ev$visible, envir)17: error <<- format(e)doTryCatch(return(expr), name, parentenv, handler) } })
TRUE18: }, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 31: 19: error = function(e) {doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
32: if (progress && is.function(pb$interrupt)) withOneRestart(expr, restarts[[1L]])
Traceback:
1: RowCumsum(valid)33:
2: pb$interrupt()FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (is_R_CMD_build() || is_R_CMD_check()) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, withRestartList(expr, restarts[-nr]) tieBreak = FALSE, verbose = verbose)20:
error <<- format(e)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
}), list(rlang_trace_top_env = knit_global()))34:
3: mc.preschedule = TRUE), error = function(e) NULL)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
48: doWithOneRestart(return(expr), restart) tau = tau, theta = th, exclusionRadius = exclusionRadius,
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 35: 21: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) error = function(e) {
if (progress && is.function(pb$interrupt)) embedded = embedded, validLib = validLib, noTime = noTime, pb$interrupt()36: if (is_R_CMD_build() || is_R_CMD_check()) withRestartList(expr, restarts) ignoreNan = ignoreNan, backend = backend)
SweepApply(theta, worker, numProcess) error <<- format(e) 4: 37:
withRestarts(with_handlers({ }), list(rlang_trace_top_env = knit_global())), function(loc) {22: setwd(wd) write_utf8(res, output %n% stdout())ComputeError(predictions$Observations, predictions$Predictions) paste0("\nQuitting from ", loc, if (!is.null(error)) unlist(SweepApply(theta, worker, numProcess)) paste0("\n", rule(), error, "\n", rule()))
for (expr in tle$exprs) { 5:
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)23: ev <- withVisible(eval(expr, envir))SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
watcher$capture_plot_and_output() knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, watcher$print_value(ev$value, ev$visible, envir)49: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", process_file(text, output) } target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
TRUE embedded = embedded, validLib = validLib, noTime = noTime, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) E = E, showPlot = TRUE)
50: 38: ignoreNan = ignoreNan, backend = backend)$predictions)evaluate::evaluate(...)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24:
51: eval(expr, envir) 6: 39: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), FUN(X[[i]], ...) output_dir = getwd(), ...)
7:
lapply(X = S, FUN = FUN, ...)25:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(expr, envir) 8: keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {52: if (options$error && options$include) 26: 0Lvweave_rmarkdown(...)withVisible(eval(expr, envir))
53:
doTryCatch(return(expr), name, parentenv, handler)27:
engine$weave(file, quiet = quiet, encoding = enc) 9: else 2LwithCallingHandlers(code, error = function (e) }, output_handler = knit_handlers(options$render, options))tryCatchOne(expr, names, parentenv, handlers[[1L]])
rlang::entrace(e), message = function (cnd)
10: 54: {tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)40:
watcher$capture_plot_and_output()55: if (on_message$capture) {in_dir(input_dir(), expr)
watcher$push(cnd)11: }tryCatchOne(expr, names, parentenv, handlers[[1L]])41:
if (on_message$silence) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, 56: invokeRestart("muffleMessage")tryCatch(expr, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } call <- conditionCall(e)tryCatchList(expr, classes, parentenv, handlers) if (!is.null(call)) { keep_message = if (is.numeric(options$message)) TRUE else options$message, }, warning = function (cnd) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) { if (identical(call[[1L]], quote(doTryCatch))) 0L if (getOption("warn") >= 2 || getOption("warn") < 0) { else 2L call <- sys.call(-4L)57: return() dcall <- deparse(call, nlines = 1L) }tryCatch({ watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options))) prefix <- paste("Error in", dcall, ": ") engine$weave(file, quiet = quiet, encoding = enc) LONG <- 75L if (on_warning$capture) {
sm <- strsplit(conditionMessage(e), "\n")[[1L]] cnd <- sanitize_call(cnd) setwd(startdir) watcher$push(cnd)42: } output <- find_vignette_product(name, by = "weave", engine = engine) if (on_warning$silence) {eng_r(options) invokeRestart("muffleWarning")
if (!have.makefile && vignette_is_tex(output)) {43: texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, error = function (cnd) { engine = engine) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], cnd <- sanitize_call(cnd) type = "b") } if (w > LONG) watcher$push(cnd) prefix <- paste0(prefix, "\n ") outputs <- c(outputs, output) } switch(on_error, continue = invokeRestart("eval_continue"), block_exec(params) else prefix <- "Error : "}, error = function(e) { msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { thisOK <<- FALSE cat(msg, file = outFile) stop = invokeRestart("eval_stop"), error = NULL)44: .Internal(printDeferredWarnings()) fails <<- c(fails, file)call_block(x) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }})
invisible(structure(msg, class = "try-error", condition = e)) file, conditionMessage(e)))})
45: 12: process_group(group)})
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)28: 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
eval(call)13: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpKpaQfn/file84573028d93d.rds")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
46: An irrecoverable exception occurred. R is aborting now ...
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(call)14: error = function(e) {FUN(X[[i]], ...)
if (progress && is.function(pb$interrupt))
30: 15: pb$interrupt()with_handlers({lapply(seq_len(cores), inner.do) if (is_R_CMD_build() || is_R_CMD_check())
for (expr in tle$exprs) {16: error <<- format(e)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) }) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()17:
doTryCatch(return(expr), name, parentenv, handler) watcher$print_value(ev$value, ev$visible, envir)
47: 18: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) {
TRUE19: if (progress && is.function(pb$interrupt)) tryCatchList(expr, classes, parentenv, handlers)}, handlers) pb$interrupt()
20: if (is_R_CMD_build() || is_R_CMD_check()) 31: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, error <<- format(e) mc.preschedule = TRUE), error = function(e) NULL)doWithOneRestart(return(expr), restart) }), list(rlang_trace_top_env = knit_global()))
48: 32: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {withOneRestart(expr, restarts[[1L]])21: if (progress && is.function(pb$interrupt)) SweepApply(theta, worker, numProcess)
pb$interrupt()22: 33: unlist(SweepApply(theta, worker, numProcess))withRestartList(expr, restarts[-nr])
if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)23: }), list(rlang_trace_top_env = knit_global())), function(loc) {34: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", setwd(wd)doWithOneRestart(return(expr), restart) write_utf8(res, output %n% stdout()) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", paste0("\nQuitting from ", loc, if (!is.null(error))
E = E, showPlot = TRUE) paste0("\n", rule(), error, "\n", rule()))
35: 24: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])eval(expr, envir)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
25: 36: eval(expr, envir)withRestartList(expr, restarts)
49: 26: process_file(text, output)
withVisible(eval(expr, envir))
37: 50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)27:
withCallingHandlers(code, error = function (e) withRestarts(with_handlers({rlang::entrace(e), message = function (cnd) for (expr in tle$exprs) {51: { ev <- withVisible(eval(expr, envir))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), watcher$capture_plot_and_output() watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (on_message$capture) { output_dir = getwd(), ...) } watcher$push(cnd)
TRUE }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (on_message$silence) {
52: 38: invokeRestart("muffleMessage")evaluate::evaluate(...) }
}, warning = function (cnd) vweave_rmarkdown(...)39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, {53: keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) stop_on_error = if (is.numeric(options$error)) options$error else {
if (getOption("warn") >= 2 || getOption("warn") < 0) { if (options$error && options$include) return()54: 0LdoTryCatch(return(expr), name, parentenv, handler)
else 2L } }, output_handler = knit_handlers(options$render, options))
55: watcher$capture_plot_and_output()40: if (on_warning$capture) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) cnd <- sanitize_call(cnd)
watcher$push(cnd)in_dir(input_dir(), expr) }56:
if (on_warning$silence) {tryCatchList(expr, classes, parentenv, handlers)41: invokeRestart("muffleWarning")in_input_dir(evaluate(code, envir = env, new_device = FALSE, }
}, error = function (cnd) 57: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch({{ keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) stop_on_error = if (is.numeric(options$error)) options$error else { watcher$capture_plot_and_output() if (options$error && options$include) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) cnd <- sanitize_call(cnd) if (!have.makefile && vignette_is_tex(output)) { 0L watcher$push(cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet) else 2L switch(on_error, continue = invokeRestart("eval_continue"), output <- find_vignette_product(name, by = "texi2pdf", }, output_handler = knit_handlers(options$render, options))) engine = engine) stop = invokeRestart("eval_stop"), error = NULL) } outputs <- c(outputs, output)
42: })}, error = function(e) {
eng_r(options) thisOK <<- FALSE28:
fails <<- c(fails, file)43: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", block_exec(params)eval(call)
file, conditionMessage(e)))44: })
call_block(x)29:
eval(call)58:
45: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 30: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpKpaQfn/file84573028d93d.rds")with_handlers({process_group(group) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
An irrecoverable exception occurred. R is aborting now ...
46: watcher$print_value(ev$value, ev$visible, envir)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { TRUE if (progress && is.function(pb$interrupt)) }, handlers) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 31: doWithOneRestart(return(expr), restart) error <<- format(e)
})32: withOneRestart(expr, restarts[[1L]])
33: 47: withRestartList(expr, restarts[-nr])with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
34: if (progress && is.function(pb$interrupt)) doWithOneRestart(return(expr), restart) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 35: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
}), list(rlang_trace_top_env = knit_global()))36:
withRestartList(expr, restarts)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 37: error = function(e) {withRestarts(with_handlers({ if (progress && is.function(pb$interrupt)) pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$print_value(ev$value, ev$visible, envir) setwd(wd) } 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: evaluate::evaluate(...)
49: 39: process_file(text, output)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,
50: stop_on_error = if (is.numeric(options$error)) options$error else {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (options$error && options$include)
0L51: else 2Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }, output_handler = knit_handlers(options$render, options)) output_dir = getwd(), ...)
40: 52: in_dir(input_dir(), expr)vweave_rmarkdown(...)
41: 53: in_input_dir(evaluate(code, envir = env, new_device = FALSE, engine$weave(file, quiet = quiet, encoding = enc) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 54: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler) 0L else 2L
}, output_handler = knit_handlers(options$render, options)))55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])42:
eng_r(options)56:
tryCatchList(expr, classes, parentenv, handlers)43:
block_exec(params)
57: 44: tryCatch({call_block(x) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)45: output <- find_vignette_product(name, by = "weave", engine = engine)process_group(group) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)
46: 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$interrupt)) } pb$interrupt() outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) { error <<- format(e) }) thisOK <<- FALSE
fails <<- c(fails, file)47: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), file, conditionMessage(e))) error = function(e) {}) if (progress && is.function(pb$interrupt))
pb$interrupt()58: if (is_R_CMD_build() || is_R_CMD_check()) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpKpaQfn/file84573028d93d.rds") error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))An irrecoverable exception occurred. R is aborting now ...
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/RtmpKpaQfn/file84573028d93d.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