Last updated on 2026-08-26 22:50:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 2.90 | 224.79 | 227.69 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.45 | 226.82 | 229.27 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 187.06 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 182.49 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 7.00 | 256.00 | 263.00 | 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 | 29.00 | 30.00 | 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 | 160.00 | 165.00 | 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
2026-08-27 06:05:43.367 R[40053:60793] 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,
Traceback:
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 1:
Traceback:
1: RowCumsum(valid)RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$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)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: 4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ignoreNan = ignoreNan, backend = backend)$predictions) tau = tau, theta = th, exclusionRadius = exclusionRadius, 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)
6: FUN(X[[i]], ...)
4: ComputeError(predictions$Observations, predictions$Predictions) 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions) 5: 9:
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatchOne(expr, names, parentenv, handlers[[1L]])
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, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
Traceback:
7: 1: lapply(X = S, FUN = FUN, ...)RowCumsum(valid)
11: 8: 8: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 9: tryCatch(expr, error = function(e) { call <- conditionCall(e) 2: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, call <- sys.call(-4L)tryCatchList(expr, classes, parentenv, handlers) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
dcall <- deparse(call, nlines = 1L) 3: prefix <- paste("Error in", dcall, ": ")SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers) if (is.na(w))
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 11: tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- sys.call(-4L) tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- conditionCall(e) dcall <- deparse(call, nlines = 1L) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") 4: type = "b") if (w > LONG) ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, if (!is.null(call)) { prefix <- paste0(prefix, "\n ") ignoreNan = ignoreNan, backend = backend)$predictions)
} if (w > LONG) prefix <- paste0(prefix, "\n ") else prefix <- "Error : " 6: FUN(X[[i]], ...) msg <- paste0(prefix, conditionMessage(e), "\n") } if (identical(call[[1L]], quote(doTryCatch))) .Internal(seterrmessage(msg[1L])) 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())
7: lapply(X = S, FUN = FUN, ...)
8: call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) } invisible(structure(msg, class = "try-error", condition = e))}) prefix <- paste("Error in", dcall, ": ")
12: doTryCatch(return(expr), name, parentenv, handler)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
LONG <- 75L
if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
sm <- strsplit(conditionMessage(e), "\n")[[1L]]13: .Internal(printDeferredWarnings())10: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers) 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 : "sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))11: } invisible(structure(msg, class = "try-error", condition = e))})
msg <- paste0(prefix, conditionMessage(e), "\n")14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {12: cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)})
22: unlist(SweepApply(theta, worker, numProcess))
13: tryCatch(expr, error = function(e) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
call <- conditionCall(e)23: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")13: LONG <- 75LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)14: 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")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
14: FUN(X[[i]], ...)
15: if (w > LONG)
lapply(seq_len(cores), inner.do)15: lapply(seq_len(cores), inner.do)
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]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: prefix <- paste0(prefix, "\n ")tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
24: } mc.preschedule = TRUE), error = function(e) NULL)eval(expr, envir)16: else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))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 (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: 25: eval(expr, envir)21:
26: SweepApply(theta, worker, numProcess)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
withVisible(eval(expr, envir))
27:
13: withCallingHandlers(code, error = function (e) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))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: 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) { invokeRestart("muffleMessage") }}, warning = function (cnd) 19: rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) {14: { if (getOption("warn") >= 2 || getOption("warn") < 0) {tryCatchList(expr, classes, parentenv, handlers) return() } watcher$capture_plot_and_output() if (on_warning$capture) {FUN(X[[i]], ...) cnd <- sanitize_call(cnd)
15:
lapply(seq_len(cores), inner.do)
16: 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) invokeRestart("muffleMessage")
22: 17: } watcher$push(cnd)doTryCatch(return(expr), name, parentenv, handler) }
}, warning = function (cnd) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: if (on_warning$silence) {tryCatchList(expr, classes, parentenv, handlers)unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 20: 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: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess) invokeRestart("muffleWarning"){ if (getOption("warn") >= 2 || getOption("warn") < 0) {
}}, error = function (cnd) 22: unlist(SweepApply(theta, worker, numProcess))withCallingHandlers(code, error = function (e)
return()23: } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd){PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), target = "Thrips_imaginis", lib = "1 73", pred = "1 73", watcher$push(cnd) E = E, showPlot = TRUE)
rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") } }24: }, warning = function (cnd) eval(expr, envir) if (on_warning$silence) { stop = invokeRestart("eval_stop"), error = NULL){ invokeRestart("muffleWarning")
}}, error = function (cnd) {}) watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) {
return() } watcher$capture_plot_and_output()25: cnd <- sanitize_call(cnd) if (on_warning$capture) {28: eval(expr, envir)eval(call)
cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) watcher$push(cnd)29: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call){eval(call)
watcher$capture_plot_and_output()
26: withVisible(eval(expr, envir))
29: cnd <- sanitize_call(cnd)30: eval(call)
watcher$push(cnd)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) {30: switch(on_error, continue = invokeRestart("eval_continue"), invokeRestart("muffleMessage") }}, warning = function (cnd) {with_handlers({ if (getOption("warn") >= 2 || getOption("warn") < 0) {with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } for (expr in tle$exprs) { stop = invokeRestart("eval_stop"), error = NULL) return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") TRUE})}, handlers)
31: doWithOneRestart(return(expr), restart)28: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
}33: 32: }, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd)withRestartList(expr, restarts[-nr]) switch(on_error, continue = invokeRestart("eval_continue"),
34: doWithOneRestart(return(expr), restart) stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])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$visible, envir) } TRUE
eval(call)withOneRestart(expr, restarts[[1L]])
}, handlers)
29: 36: 33: eval(call)withRestartList(expr, restarts)
31: 37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withRestartList(expr, restarts[-nr])
doWithOneRestart(return(expr), restart) 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) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
watcher$print_value(ev$value, ev$visible, envir) }34: 38: evaluate::evaluate(...)doWithOneRestart(return(expr), restart)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {
35: if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
41: 30: in_input_dir(evaluate(code, envir = env, new_device = FALSE, TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38:
36: withRestartList(expr, restarts)with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
evaluate::evaluate(...)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
33: 37: withRestartList(expr, restarts[-nr])39: keep_message = if (is.numeric(options$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)))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withRestarts(with_handlers({ 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
42: eng_r(options)
43: else 2L34: for (expr in tle$exprs) {doWithOneRestart(return(expr), restart) }, output_handler = knit_handlers(options$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$render, options)))
42: eng_r(options)block_exec(params)
35: ev <- withVisible(eval(expr, envir))
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) }
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({44:
call_block(x) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {
for (expr in tle$exprs) {45: process_group(group)
46: if (options$error && options$include) 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) {43: 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: if (progress && is.function(pb$interrupt)) block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) ev <- withVisible(eval(expr, envir)) if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
}) watcher$print_value(ev$value, ev$visible, envir)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
in_dir(input_dir(), expr)47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), TRUE49: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
process_file(text, output) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) keep_message = if (is.numeric(options$message)) TRUE else options$message, 38: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L
49: 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) else 2Levaluate::evaluate(...)process_file(text, output) }, output_handler = knit_handlers(options$render, options)))
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 { 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$include)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: 51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 51: 42: output_dir = getwd(), ...)eng_r(options)
call_block(x)
45: process_group(group)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
if (progress && is.function(pb$interrupt)) 43: pb$interrupt()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), if (is_R_CMD_build() || is_R_CMD_check()) block_exec(params)54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers) output_dir = getwd(), ...)
44: error <<- format(e)
call_block(x)
45: 57: process_group(group)52: tryCatch({
})
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: engine$weave(file, quiet = quiet, encoding = enc)tryCatchOne(expr, names, parentenv, handlers[[1L]]) setwd(startdir)46: output <- find_vignette_product(name, by = "weave", engine = engine)
56: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() error = function(e) {
if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)57: }) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatch({
error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", engine$weave(file, quiet = quiet, encoding = enc)47: }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 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: engine = engine) setwd(wd) } write_utf8(res, output %n% stdout()) outputs <- c(outputs, output) paste0("\nQuitting from ", loc, if (!is.null(error)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) file, conditionMessage(e)))
})
}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt()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/RtmpLrEtBD/file81dd878e697.rds") if (is_R_CMD_build() || is_R_CMD_check()) 49: process_file(text, output) error <<- format(e) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpLrEtBD/file81dd878e697.rds")
An irrecoverable exception occurred. R is aborting now ...
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
An irrecoverable exception occurred. R is aborting now ...
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
}), 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()))52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)}, 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(), ...)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpLrEtBD/file81dd878e697.rds")
56: tryCatchList(expr, classes, parentenv, handlers)
An irrecoverable exception occurred. R is aborting now ...
57: tryCatch({ engine$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/RtmpLrEtBD/file81dd878e697.rds")
An irrecoverable exception occurred. R is aborting now ...
rm: /Volumes/Temp/tmp/Rtmpvp89h7/libloc_219_a0a8cf4defec7e8d.rds: Invalid argument
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