Last updated on 2026-08-24 01:51:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.51 | 223.48 | 226.99 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.47 | 227.68 | 230.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 181.30 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 260.00 | 265.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.09 | 204.94 | 208.03 | 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 | 4.00 | 127.00 | 131.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 25.00 | 26.00 | 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 | 161.00 | 166.00 | 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
2026-08-24 11:01:21.298 R[48522:71986] 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$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
Traceback:
Traceback:
1:
Traceback:
1: RowCumsum(valid)RowCumsum(valid) embedded = embedded, validLib = validLib, noTime = noTime, 1: ignoreNan = ignoreNan, backend = backend)$predictions)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 2: verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, RowCumsum(valid) embedded = embedded, validLib = validLib, noTime = noTime, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
2: 6: FUN(X[[i]], ...)
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
7: lapply(X = S, FUN = FUN, ...)
8: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 4: 3: ComputeError(predictions$Observations, predictions$Predictions)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
doTryCatch(return(expr), name, parentenv, handler) tau = tau, theta = th, exclusionRadius = exclusionRadius,
ignoreNan = ignoreNan, backend = backend) 5: 9:
4: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatchOne(expr, names, parentenv, handlers[[1L]]) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ComputeError(predictions$Observations, predictions$Predictions)
embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) 5: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)10: tryCatchList(expr, classes, parentenv, handlers)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)$predictions)11:
tryCatch(expr, error = function(e) { call <- conditionCall(e)
6:
7: 4: lapply(X = S, FUN = FUN, ...)FUN(X[[i]], ...)
ComputeError(predictions$Observations, predictions$Predictions)
7:
8: lapply(X = S, FUN = FUN, ...)
5: doTryCatch(return(expr), name, parentenv, handler)
9: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)tryCatchList(expr, classes, parentenv, handlers)
if (!is.null(call)) { 8: if (identical(call[[1L]], quote(doTryCatch))) doTryCatch(return(expr), name, parentenv, handler)
6: FUN(X[[i]], ...)11:
tryCatch(expr, error = function(e) { call <- sys.call(-4L) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) dcall <- deparse(call, nlines = 1L) 7: lapply(X = S, FUN = FUN, ...) call <- conditionCall(e)
prefix <- paste("Error in", dcall, ": ") 8: doTryCatch(return(expr), name, parentenv, handler) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
if (!is.null(call)) { 9: 10: tryCatchList(expr, classes, parentenv, handlers) if (identical(call[[1L]], quote(doTryCatch)))
tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)11:
10: prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], LONG <- 75LtryCatchList(expr, classes, parentenv, handlers) type = "b")tryCatch(expr, error = function(e) { if (w > LONG)
call <- conditionCall(e) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 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)) if (!is.null(call)) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")})11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (identical(call[[1L]], quote(doTryCatch))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) type = "b") dcall <- deparse(call, nlines = 1L) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) if (w > LONG) prefix <- paste("Error in", dcall, ": ") prefix <- paste0(prefix, "\n ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
prefix <- paste("Error in", dcall, ": ")14: } LONG <- 75L else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (is.na(w)) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) sm <- strsplit(conditionMessage(e), "\n")[[1L]]})FUN(X[[i]], ...) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 15: if (is.na(w)) lapply(seq_len(cores), inner.do) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") type = "b")16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (w > LONG) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)19:
tryCatchList(expr, classes, parentenv, handlers)13: if (w > LONG) prefix <- paste0(prefix, "\n ") 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)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) .Internal(printDeferredWarnings())
14:
FUN(X[[i]], ...)
} 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())15: 20: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: lapply(seq_len(cores), inner.do) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)eval(expr, envir) invisible(structure(msg, class = "try-error", condition = e))
})26:
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: withVisible(eval(expr, envir))
16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
27: 16: 14: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)17:
doTryCatch(return(expr), name, parentenv, handler)
17: doTryCatch(return(expr), name, parentenv, handler)
18: FUN(X[[i]], ...)18: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
15:
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) lapply(seq_len(cores), inner.do)
19: tryCatchList(expr, classes, parentenv, handlers)
{ watcher$capture_plot_and_output() if (on_message$capture) {
20: 19: tryCatchList(expr, classes, parentenv, handlers) watcher$push(cnd)16: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
20: 23: } if (on_message$silence) {17: doTryCatch(return(expr), name, parentenv, handler)
18: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, invokeRestart("muffleMessage")
24: eval(expr, envir)
25: mc.preschedule = TRUE), error = function(e) NULL)tryCatchOne(expr, names, parentenv, handlers[[1L]])
eval(expr, envir) }
19: tryCatchList(expr, classes, parentenv, handlers)
20: 26: 21: }, warning = function (cnd) {withVisible(eval(expr, envir))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (getOption("warn") >= 2 || getOption("warn") < 0) { mc.preschedule = TRUE), error = function(e) NULL) return() }SweepApply(theta, worker, numProcess)
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) { watcher$capture_plot_and_output() invokeRestart("muffleMessage") if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)22: 21: }unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { } if (on_warning$silence) { invokeRestart("muffleMessage")SweepApply(theta, worker, numProcess) invokeRestart("muffleWarning")}, warning = function (cnd) }}, warning = function (cnd)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: }}, error = 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)})
28: eval(call)
29: if (getOption("warn") >= 2 || getOption("warn") < 0) {eval(expr, envir)eval(call) return() } watcher$capture_plot_and_output() if (on_warning$capture) {
cnd <- sanitize_call(cnd){25: watcher$push(cnd)eval(expr, envir) if (getOption("warn") >= 2 || getOption("warn") < 0) { } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) return() switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
} watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)
30: }30: with_handlers({ if (on_warning$silence) {with_handlers({ for (expr in tle$exprs) {
for (expr in tle$exprs) {26: withVisible(eval(expr, envir)) invokeRestart("muffleWarning")
ev <- withVisible(eval(expr, envir)) } ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$capture_plot_and_output()}, error = function (cnd) watcher$print_value(ev$value, ev$visible, envir) } watcher$print_value(ev$value, ev$visible, envir){ TRUE27: }, handlers)
watcher$capture_plot_and_output() } TRUE cnd <- sanitize_call(cnd)}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])31:
doWithOneRestart(return(expr), restart)34:
watcher$push(cnd)32: withOneRestart(expr, restarts[[1L]])withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()doWithOneRestart(return(expr), restart)
33: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36:
if (on_message$capture) { watcher$push(cnd)withRestartList(expr, restarts)withRestartList(expr, restarts[-nr]) }
28:
eval(call)
29: eval(call)
30: 34: 37: doWithOneRestart(return(expr), restart)with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } if (on_message$silence) {35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: invokeRestart("muffleMessage")withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withRestarts(with_handlers({ }}, warning = function (cnd) TRUE watcher$capture_plot_and_output(){ watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
}, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) { for (expr in tle$exprs) { return()
31: } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)38: evaluate::evaluate(...)
doWithOneRestart(return(expr), restart) ev <- withVisible(eval(expr, envir))39:
watcher$push(cnd)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, } if (on_warning$silence) { invokeRestart("muffleWarning") watcher$capture_plot_and_output()32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: 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$visible, envir) } }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$print_value(ev$value, ev$visible, envir) TRUE watcher$push(cnd) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
switch(on_error, continue = invokeRestart("eval_continue"), 38: stop = invokeRestart("eval_stop"), error = NULL)evaluate::evaluate(...)}) stop_on_error = if (is.numeric(options$error)) options$error else {
28: eval(call)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } if (options$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$render, options))) TRUE
42: 39: }, handlers)eng_r(options)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
43: block_exec(params)
keep_message = if (is.numeric(options$message)) TRUE else options$message,
38: evaluate::evaluate(...)
31: 44: call_block(x)39: doWithOneRestart(return(expr), restart)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
40: in_dir(input_dir(), expr) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
45: 32:
withOneRestart(expr, restarts[[1L]])41: 40: in_dir(input_dir(), expr)
33: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0LwithRestartList(expr, restarts[-nr])
process_group(group)
else 2L34:
41: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)in_input_dir(evaluate(code, envir = env, new_device = FALSE, 46: for (expr in tle$exprs) {
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is_R_CMD_build() || is_R_CMD_check()) 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, error <<- format(e) pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is_R_CMD_build() || is_R_CMD_check()) stop_on_error = if (is.numeric(options$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) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) if (options$error && options$include)
}) 0L
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() else 2L }, output_handler = knit_handlers(options$render, options)))
if (is_R_CMD_build() || is_R_CMD_check()) 41: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt)) pb$interrupt() keep_message = if (is.numeric(options$message)) TRUE else options$message, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L setwd(wd) write_utf8(res, output %n% stdout()) if (is_R_CMD_build() || is_R_CMD_check()) else 2L42: error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) }, output_handler = knit_handlers(options$render, options)))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
42: eng_r(options)52:
vweave_rmarkdown(...)49: eng_r(options)process_file(text, output)
43: block_exec(params)
44:
call_block(x)43:
block_exec(params)53: 50:
44: call_block(x)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)45:
process_group(group)
45: process_group(group)51:
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()46: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) if (is_R_CMD_build() || is_R_CMD_check())
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 55: 52: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {vweave_rmarkdown(...)
53: error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), list(rlang_trace_top_env = knit_global())), function(loc) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
engine$weave(file, quiet = quiet, encoding = enc)56:
54: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers) }), list(rlang_trace_top_env = knit_global()))
57:
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) setwd(wd)55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
output <- find_vignette_product(name, by = "texi2pdf", if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 56: paste0("\n", rule(), error, "\n", rule())) engine = engine)tryCatchList(expr, classes, parentenv, handlers)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {57: tryCatch({ setwd(wd)
write_utf8(res, output %n% stdout()) engine$weave(file, quiet = quiet, encoding = enc) paste0("\nQuitting from ", loc, if (!is.null(error)) setwd(startdir) } paste0("\n", rule(), error, "\n", rule())) outputs <- c(outputs, output) output <- find_vignette_product(name, by = "weave", engine = engine)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, error = function(e) { if (!have.makefile && vignette_is_tex(output)) {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(), ...)
thisOK <<- FALSE fails <<- c(fails, file)52: texi2pdf(file = output, clean = FALSE, quiet = quiet)vweave_rmarkdown(...)
53: output <- find_vignette_product(name, by = "texi2pdf", engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)49: engine = engine) } outputs <- c(outputs, output)process_file(text, output)
}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
58: file, conditionMessage(e)))tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 50: })knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: 58: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpySwl5g/file83cc71d96e8b.rds")
An irrecoverable exception occurred. R is aborting now ...
output_dir = getwd(), ...) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpySwl5g/file83cc71d96e8b.rds")
52: vweave_rmarkdown(...)
56: 53: An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))55: })
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpySwl5g/file83cc71d96e8b.rds")
An irrecoverable exception occurred. R is aborting now ...
tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/RtmpySwl5g/file83cc71d96e8b.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