Last updated on 2026-08-10 10:50:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.35 | 222.44 | 225.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.31 | 221.99 | 224.30 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 186.14 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 131.00 | 136.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 3.74 | 206.25 | 209.99 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.45 | 205.25 | 208.70 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 41.00 | 42.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 5.00 | 164.00 | 169.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-10 19:18:40.375 R[40659:59215] 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$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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)
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: 6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
Traceback:
1:
ComputeError(predictions$Observations, predictions$Predictions)
5: 8: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 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, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend) embedded = embedded, validLib = validLib, noTime = noTime,
4: doTryCatch(return(expr), name, parentenv, handler)
9: ignoreNan = ignoreNan, backend = backend)$predictions)ComputeError(predictions$Observations, predictions$Predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 8: doTryCatch(return(expr), name, parentenv, handler)
9: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)10:
tryCatchList(expr, classes, parentenv, handlers) 6:
11: tryCatch(expr, error = function(e) {FUN(X[[i]], ...) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 7: lapply(X = S, FUN = FUN, ...)
Traceback:
call <- sys.call(-4L) 1: dcall <- deparse(call, nlines = 1L)RowCumsum(valid)
call <- conditionCall(e) 8: prefix <- paste("Error in", dcall, ": ") if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler)
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], 9: type = "b")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (w > LONG) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : "10: msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { 2: tryCatchList(expr, classes, parentenv, handlers) 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])) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
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)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
11: 14: FUN(X[[i]], ...)
15:
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(seq_len(cores), inner.do)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatch(expr, error = function(e) { call <- conditionCall(e) verbose = verbose) if (!is.null(call)) {
16: 3:
13: if (identical(call[[1L]], quote(doTryCatch))) SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
17: if (w > LONG) 14: doTryCatch(return(expr), name, parentenv, handler)
FUN(X[[i]], ...) 4: ComputeError(predictions$Observations, predictions$Predictions)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])15: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...) prefix <- paste0(prefix, "\n ")19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
} 8: 21: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess)
9: lapply(seq_len(cores), inner.do)
16:
22: else prefix <- "Error : "tryCatchOne(expr, names, parentenv, handlers[[1L]])parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)unlist(SweepApply(theta, worker, numProcess))
msg <- paste0(prefix, conditionMessage(e), "\n")17: doTryCatch(return(expr), name, parentenv, handler) .Internal(seterrmessage(msg[1L]))
10: tryCatchList(expr, classes, parentenv, handlers)
11: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!silent && isTRUE(getOption("show.error.messages"))) {23: tryCatch(expr, error = function(e) { cat(msg, file = outFile)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
call <- conditionCall(e) E = E, showPlot = TRUE)
24: eval(expr, envir)
25: if (!is.null(call)) {19: eval(expr, envir) if (identical(call[[1L]], quote(doTryCatch))) .Internal(printDeferredWarnings())
}26: call <- sys.call(-4L)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) {tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L) invisible(structure(msg, class = "try-error", condition = e))})
12: if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)20: prefix <- paste("Error in", dcall, ": ") } LONG <- 75LtryCatch(parallel::mclapply(values, worker, mc.cores = cores, sm <- strsplit(conditionMessage(e), "\n")[[1L]] mc.preschedule = TRUE), error = function(e) NULL)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) } invisible(structure(msg, class = "try-error", condition = e))})
21: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))SweepApply(theta, worker, numProcess){14: watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)FUN(X[[i]], ...)
15: watcher$push(cnd)22:
switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})lapply(seq_len(cores), inner.do)
unlist(SweepApply(theta, worker, numProcess))28: 14:
FUN(X[[i]], ...)
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 16: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)eval(call) E = E, showPlot = TRUE)
15: 17: lapply(seq_len(cores), inner.do)doTryCatch(return(expr), name, parentenv, handler)
24: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
eval(expr, envir)
25: eval(expr, envir)19: tryCatchList(expr, classes, parentenv, handlers)
26: withVisible(eval(expr, envir))
20:
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {29: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 16: eval(call)
30: mc.preschedule = TRUE), error = function(e) NULL)with_handlers({
watcher$capture_plot_and_output() for (expr in tle$exprs) {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) ev <- withVisible(eval(expr, envir))21: watcher$capture_plot_and_output()SweepApply(theta, worker, numProcess) if (on_message$capture) {
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)
17: watcher$print_value(ev$value, ev$visible, envir)doTryCatch(return(expr), name, parentenv, handler) }24: eval(expr, envir)
TRUE25:
eval(expr, envir)
26: withVisible(eval(expr, envir))18: }, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
watcher$push(cnd)31: } if (on_message$silence) {doWithOneRestart(return(expr), restart)
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
invokeRestart("muffleMessage")
}32: withOneRestart(expr, restarts[[1L]])
{33: withRestartList(expr, restarts[-nr])}, warning = function (cnd) {
21: SweepApply(theta, worker, numProcess) watcher$capture_plot_and_output()
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (on_message$capture) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 34: E = E, showPlot = TRUE) watcher$push(cnd)doWithOneRestart(return(expr), restart)
}24: if (on_message$silence) { invokeRestart("muffleMessage")eval(expr, envir)
if (getOption("warn") >= 2 || getOption("warn") < 0) {
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: }withRestartList(expr, restarts)}, warning = function (cnd) 25: { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)eval(expr, envir)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
if (getOption("warn") >= 2 || getOption("warn") < 0) {26: return() }withVisible(eval(expr, envir))
} TRUE27: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$push(cnd)
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$capture_plot_and_output()38: watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") } } if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)}, warning = function (cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)evaluate::evaluate(...){
if (on_warning$silence) {39: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message, if (on_warning$capture) { watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE invokeRestart("muffleWarning") stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L } }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
}, error = function (cnd) }, handlers) cnd <- sanitize_call(cnd)
watcher$push(cnd){31: }43: block_exec(params) if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
cnd <- sanitize_call(cnd)44: call_block(x)
45: process_group(group)
doWithOneRestart(return(expr), restart) watcher$push(cnd) watcher$push(cnd)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) switch(on_error, continue = invokeRestart("eval_continue"), switch(on_error, continue = invokeRestart("eval_continue"), pb$interrupt() stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: 32: withOneRestart(expr, restarts[[1L]])
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))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:
stop = invokeRestart("eval_stop"), error = NULL) watcher$capture_plot_and_output()})
28: eval(call)
29: eval(call)33: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) watcher$print_value(ev$value, ev$visible, envir) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) } paste0("\n", rule(), error, "\n", rule())) TRUE30: withRestartList(expr, restarts[-nr])}, handlers)with_handlers({
31:
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)34: doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])31:
34: doWithOneRestart(return(expr), restart)
49: 35: process_file(text, output)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
doWithOneRestart(return(expr), restart)
36: withRestartList(expr, restarts)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: 36: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withRestartList(expr, restarts)37:
output_dir = getwd(), ...)withRestarts(with_handlers({32: for (expr in tle$exprs) {37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]])
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
33: withRestartList(expr, restarts[-nr]) if (options$error && options$include)
52: 0Lvweave_rmarkdown(...)39: else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 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, 53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler) stop_on_error = if (is.numeric(options$error)) options$error else { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
55: if (options$error && options$include) if (options$error && options$include) 0L else 2L 0L34: }, output_handler = knit_handlers(options$render, options))) else 2L }, output_handler = knit_handlers(options$render, options))doWithOneRestart(return(expr), restart)
40: in_dir(input_dir(), expr)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])42: 41: eng_r(options)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
36: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withRestartList(expr, restarts)
56: 37: tryCatchList(expr, classes, parentenv, handlers)
57: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {withRestarts(with_handlers({43: block_exec(params)
if (options$error && options$include) 44: 0L else 2Lcall_block(x)tryCatch({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }, output_handler = knit_handlers(options$render, options)))
45: engine$weave(file, quiet = quiet, encoding = enc)42: } TRUEeng_r(options)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)process_group(group)
setwd(startdir)
38: evaluate::evaluate(...)46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)43: block_exec(params) pb$interrupt()
39: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {47: if (options$error && options$include) 0L }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), outputs <- c(outputs, output) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) else 2L}, error = function(e) { }, output_handler = knit_handlers(options$render, options))
thisOK <<- FALSE40: 44: error <<- format(e)call_block(x)
45: process_group(group) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})in_dir(input_dir(), expr)
}), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { pb$interrupt()58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (progress && is.function(pb$interrupt))
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpi9fzaU/file6b7a3758e967.rds")
pb$interrupt()An irrecoverable exception occurred. R is aborting now ...
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) keep_message = if (is.numeric(options$message)) TRUE else options$message, paste0("\n", rule(), error, "\n", rule())) error <<- format(e)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) process_file(text, output)
0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: 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$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)eng_r(options)
43: block_exec(params)
44: call_block(x)
})
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 45: process_group(group)
46: 57: pb$interrupt()tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 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())) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() texi2pdf(file = output, clean = FALSE, quiet = quiet) if (is_R_CMD_build() || is_R_CMD_check()) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 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", error <<- format(e) file, conditionMessage(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()49: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)process_file(text, output) }), list(rlang_trace_top_env = knit_global())), function(loc) {
})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", setwd(wd) write_utf8(res, output %n% stdout()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpi9fzaU/file6b7a3758e967.rds")
An irrecoverable exception occurred. R is aborting now ...
paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)50:
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
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$weave(file, quiet = quiet, encoding = enc)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$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$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) {54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) 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/Rtmpi9fzaU/file6b7a3758e967.rds")
An irrecoverable exception occurred. R is aborting now ...
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/Rtmpi9fzaU/file6b7a3758e967.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