Last updated on 2026-09-03 14:53:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.45 | 222.09 | 225.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.50 | 237.83 | 240.33 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.65 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 186.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 135.00 | 140.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.92 | 207.03 | 210.95 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.39 | 203.63 | 207.02 | 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 | 137.00 | 144.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 26.00 | 27.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 5.00 | 164.00 | 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
2026-09-03 19:55:46.616 R[47670:70397] 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
Traceback:
1: RowCumsum(valid)
2:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tau = tau, theta = th, exclusionRadius = exclusionRadius, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: embedded = embedded, validLib = validLib, noTime = noTime, 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$Predictions)
ignoreNan = ignoreNan, backend = backend)
4: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
ComputeError(predictions$Observations, predictions$Predictions)
5: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, embedded = embedded, validLib = validLib, noTime = noTime, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)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, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: 7: lapply(X = S, FUN = FUN, ...) 6:
8: FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9:
Traceback:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 1: 10: RowCumsum(valid)tryCatchList(expr, classes, parentenv, handlers)lapply(X = S, FUN = FUN, ...)
2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 8: tieBreak = FALSE, verbose = verbose)10: doTryCatch(return(expr), name, parentenv, handler)
tryCatchList(expr, classes, parentenv, handlers)
9: 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)10: dcall <- deparse(call, nlines = 1L)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { 3: 11: call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") call <- sys.call(-4L) if (is.na(w)) dcall <- deparse(call, nlines = 1L) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")tryCatch(expr, error = function(e) { prefix <- paste("Error in", dcall, ": ")SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- conditionCall(e) if (w > LONG) LONG <- 75L embedded = embedded, validLib = validLib, noTime = noTime, prefix <- paste0(prefix, "\n ") if (!is.null(call)) { ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) 5: if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) .Internal(printDeferredWarnings())SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: } .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))})
invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
doTryCatch(return(expr), name, parentenv, handler)14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
14: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])FUN(X[[i]], ...)
15:
lapply(seq_len(cores), inner.do)15: lapply(seq_len(cores), inner.do)
16:
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)14:
17: FUN(X[[i]], ...)
17: 10: 15: doTryCatch(return(expr), name, parentenv, handler)lapply(seq_len(cores), inner.do)
tryCatchList(expr, classes, parentenv, handlers)18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11:
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
19: 20: tryCatch(expr, error = function(e) {tryCatchList(expr, classes, parentenv, handlers)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, call <- conditionCall(e)17: mc.preschedule = TRUE), error = function(e) NULL)doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: SweepApply(theta, worker, numProcess)
if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)22: prefix <- paste("Error in", dcall, ": ") mc.preschedule = TRUE), error = function(e) NULL)
21: unlist(SweepApply(theta, worker, numProcess))19: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]SweepApply(theta, worker, numProcess) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
22: tryCatchList(expr, classes, parentenv, handlers)
if (is.na(w)) 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: unlist(SweepApply(theta, worker, numProcess)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) 23: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", prefix <- paste0(prefix, "\n ")
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 23: }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
E = E, showPlot = TRUE) else prefix <- "Error : "24:
msg <- paste0(prefix, conditionMessage(e), "\n")24: eval(expr, envir) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } E = E, showPlot = TRUE) invisible(structure(msg, class = "try-error", condition = e))25: eval(expr, envir)
26: withVisible(eval(expr, envir))eval(expr, envir)24:
eval(expr, envir)
25: 27:
eval(expr, envir)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) }){
watcher$capture_plot_and_output()25: eval(expr, envir)
26: if (on_message$capture) {
watcher$push(cnd)12: withVisible(eval(expr, envir))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
27: 26: withCallingHandlers(code, error = function (e) }13: withVisible(eval(expr, envir))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
27: if (on_message$silence) { invokeRestart("muffleMessage")withCallingHandlers(code, error = function (e)
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
}}, warning = function (cnd) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()16: { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)rlang::entrace(e), message = function (cnd) if (on_warning$capture) { if (on_message$capture) { cnd <- sanitize_call(cnd)
watcher$push(cnd) watcher$push(cnd)17: }{ } watcher$capture_plot_and_output()doTryCatch(return(expr), name, parentenv, handler) if (on_warning$silence) { invokeRestart("muffleWarning") if (on_message$silence) {
if (on_message$capture) { watcher$push(cnd) }18: } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) }, error = function (cnd) { invokeRestart("muffleMessage") if (getOption("warn") >= 2 || getOption("warn") < 0) {{ }tryCatchOne(expr, names, parentenv, handlers[[1L]])
}, warning = function (cnd) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
19: 28: eval(call)
{29: eval(call)tryCatchList(expr, classes, parentenv, handlers)
return() } watcher$capture_plot_and_output()
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
if (on_warning$capture) { if (getOption("warn") >= 2 || getOption("warn") < 0) {30: return()with_handlers({ } watcher$capture_plot_and_output() if (on_warning$capture) {22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", cnd <- sanitize_call(cnd) for (expr in tle$exprs) { watcher$push(cnd) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: {withOneRestart(expr, restarts[[1L]]) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) E = E, showPlot = TRUE)33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
24: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})35:
watcher$push(cnd)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
28: eval(expr, envir)36: }eval(call) if (on_warning$silence) {
invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
watcher$push(cnd)25: withRestartList(expr, restarts)eval(expr, envir)
switch(on_error, continue = invokeRestart("eval_continue"), 29:
26: stop = invokeRestart("eval_stop"), error = NULL)withVisible(eval(expr, envir))eval(call)
})
28:
37: 30: 27: withRestarts(with_handlers({with_handlers({eval(call)
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withCallingHandlers(code, error = function (e) watcher$capture_plot_and_output() for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))29: watcher$print_value(ev$value, ev$visible, envir)rlang::entrace(e), message = function (cnd) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])eval(call)
30: watcher$capture_plot_and_output(){
watcher$capture_plot_and_output()with_handlers({ if (on_message$capture) { watcher$push(cnd) for (expr in tle$exprs) {33: watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts[-nr]) }
34: } if (on_message$silence) {doWithOneRestart(return(expr), restart) invokeRestart("muffleMessage")
}35: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd)
ev <- withVisible(eval(expr, envir))36: {38: evaluate::evaluate(...)
withRestartList(expr, restarts)39: watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L}) }, output_handler = knit_handlers(options$render, options))
37:
40: in_dir(input_dir(), expr) watcher$capture_plot_and_output()withRestarts(with_handlers({ watcher$print_value(ev$value, ev$visible, envir)28: }eval(call)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
for (expr in tle$exprs) {29: eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, TRUE keep_message = if (is.numeric(options$message)) TRUE else options$message, ev <- withVisible(eval(expr, envir))}, handlers) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
30: stop_on_error = if (is.numeric(options$error)) options$error else { }with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
TRUE
39: }, handlers)31: doWithOneRestart(return(expr), restart)
if (options$error && options$include)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 0L else 2L32: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L }, output_handler = knit_handlers(options$render, options)))withOneRestart(expr, restarts[[1L]]) else 2L
31: doWithOneRestart(return(expr), restart)42:
eng_r(options)32: withOneRestart(expr, restarts[[1L]])
}, output_handler = knit_handlers(options$render, options))33:
withRestartList(expr, restarts[-nr])43:
block_exec(params)34: 33:
doWithOneRestart(return(expr), restart)withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)44:
call_block(x)
45: process_group(group)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 35: error <<- format(e) })
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
47: 40: in_dir(input_dir(), expr)
41: 38: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, 36: evaluate::evaluate(...)withRestartList(expr, restarts)
39:
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, } TRUE if (progress && is.function(pb$interrupt)) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) stop_on_error = if (is.numeric(options$error)) options$error else { stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) pb$interrupt() 0L if (is_R_CMD_build() || is_R_CMD_check())
else 2L38: if (options$error && options$include) evaluate::evaluate(...) }, output_handler = knit_handlers(options$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) error <<- format(e) 0L 0L else 2L
else 2L }, output_handler = knit_handlers(options$render, options)))
39: }, output_handler = knit_handlers(options$render, options)))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }), list(rlang_trace_top_env = knit_global()))
42:
42: eng_r(options)
keep_message = if (is.numeric(options$message)) TRUE else options$message, 43: stop_on_error = if (is.numeric(options$error)) options$error else {block_exec(params)eng_r(options) if (options$error && options$include)
0L else 2L48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
43: 44: block_exec(params)
error = function(e) {44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options)) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
40: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) call_block(x)
in_dir(input_dir(), expr)45:
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()process_group(group)
41: error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 46: write_utf8(res, output %n% stdout()) paste0("\n", rule(), error, "\n", rule()))withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), paste0("\nQuitting from ", loc, if (!is.null(error)) output_dir = getwd(), ...)
52: keep_message = if (is.numeric(options$message)) TRUE else options$message, error = function(e) { paste0("\n", rule(), error, "\n", rule())) if (progress && is.function(pb$interrupt)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)vweave_rmarkdown(...)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55:
stop_on_error = if (is.numeric(options$error)) options$error else { pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is_R_CMD_build() || is_R_CMD_check())
if (options$error && options$include) 0L56: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), else 2L error <<- format(e) }, output_handler = knit_handlers(options$render, options)))
output_dir = getwd(), ...)42: eng_r(options)
43: block_exec(params) })
47: 44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout())call_block(x) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatchList(expr, classes, parentenv, handlers)52:
vweave_rmarkdown(...)
45:
process_group(group)53: 57: engine$weave(file, quiet = quiet, encoding = enc)
54: 49:
doTryCatch(return(expr), name, parentenv, handler)tryCatch({46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
error = function(e) {55: process_file(text, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])
texi2pdf(file = output, clean = FALSE, quiet = quiet) if (progress && is.function(pb$interrupt))
output <- find_vignette_product(name, by = "texi2pdf", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) 50: 56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine = engine) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) } if (!have.makefile && vignette_is_tex(output)) { outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), error <<- format(e) output_dir = getwd(), ...) texi2pdf(file = output, clean = FALSE, quiet = quiet) fails <<- c(fails, file)
output <- find_vignette_product(name, by = "texi2pdf", 52: vweave_rmarkdown(...) engine = engine) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", } outputs <- c(outputs, output) file, conditionMessage(e))) })
}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)47: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 53: })with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
58: file, conditionMessage(e))) error = function(e) {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdbuG2K/file817558554d59.rds")
An irrecoverable exception occurred. R is aborting now ...
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()))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)58: 48: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), output <- find_vignette_product(name, by = "texi2pdf", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdbuG2K/file817558554d59.rds")
An irrecoverable exception occurred. R is aborting now ...
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())) engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)}, 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$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})57: tryCatch({ engine$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/RtmpdbuG2K/file817558554d59.rds")
An irrecoverable exception occurred. R is aborting now ...
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/RtmpdbuG2K/file817558554d59.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