Last updated on 2026-08-22 17:50:37 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 | 2.34 | 233.75 | 236.09 | 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 | 3.27 | 210.37 | 213.64 | 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 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 7.00 | 160.00 | 167.00 | 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
2026-08-23 01:58:51.305 R[52733:77251] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
Traceback:
1:
Traceback:
RowCumsum(valid)
2:
Traceback:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 1: verbose = verbose) 1: tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)RowCumsum(valid)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...) 4: ComputeError(predictions$Observations, predictions$Predictions)RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
2: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
7: 3: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(X = S, FUN = FUN, ...) verbose = verbose)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) ignoreNan = ignoreNan, backend = backend)
10:
5: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tryCatchList(expr, classes, parentenv, handlers)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 11: embedded = embedded, validLib = validLib, noTime = noTime, tau = tau, theta = th, exclusionRadius = exclusionRadius, 4: ComputeError(predictions$Observations, predictions$Predictions)
5: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 5: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)$predictions)
embedded = embedded, validLib = validLib, noTime = noTime, tryCatch(expr, error = function(e) { ignoreNan = ignoreNan, backend = backend)$predictions) call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) 6: dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")FUN(X[[i]], ...) 6:
7: lapply(X = S, FUN = FUN, ...)
8: LONG <- 75LdoTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e)
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } 7: lapply(X = S, FUN = FUN, ...) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) else prefix <- "Error : " if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
if (!is.null(call)) { .Internal(printDeferredWarnings()) } if (identical(call[[1L]], quote(doTryCatch))) 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: 8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") invisible(structure(msg, class = "try-error", condition = e)) if (w > LONG) }) prefix <- paste0(prefix, "\n ") }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
13: if (!silent && isTRUE(getOption("show.error.messages"))) { call <- sys.call(-4L)sendMaster(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)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
14: 17: FUN(X[[i]], ...)
15: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") cat(msg, file = outFile) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) lapply(seq_len(cores), inner.do) .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } invisible(structure(msg, class = "try-error", condition = e))
16: })parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18:
type = "b")18: if (w > LONG) prefix <- paste0(prefix, "\n ")12: } else prefix <- "Error : "tryCatchOne(expr, names, parentenv, handlers[[1L]])try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
tryCatchOne(expr, names, parentenv, handlers[[1L]])19:
msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)19: tryCatchList(expr, classes, parentenv, handlers)
13: .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))})
14: 12: FUN(X[[i]], ...)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15:
13: lapply(seq_len(cores), inner.do)tryCatchList(expr, classes, parentenv, handlers)20: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
20:
16: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do) mc.preschedule = TRUE), error = function(e) NULL)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
mc.preschedule = TRUE), error = function(e) NULL)17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
21: 17: doTryCatch(return(expr), name, parentenv, handler)20:
SweepApply(theta, worker, numProcess)
18: 21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 22: unlist(SweepApply(theta, worker, numProcess))tryCatchList(expr, classes, parentenv, handlers)SweepApply(theta, worker, numProcess)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
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)
20: 23: mc.preschedule = TRUE), error = function(e) NULL)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 24: eval(expr, envir)
E = E, showPlot = TRUE)25: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, eval(expr, envir)
mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
26:
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: withVisible(eval(expr, envir))eval(expr, envir)
21: 25: SweepApply(theta, worker, numProcess)24: eval(expr, envir)
25: eval(expr, envir)
eval(expr, envir)27: withCallingHandlers(code, error = function (e) 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) {
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", watcher$push(cnd)rlang::entrace(e), message = function (cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() }{ E = E, showPlot = TRUE)
24: watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)eval(expr, envir) if (on_message$capture) { watcher$push(cnd)26: withVisible(eval(expr, envir))
27: } watcher$push(cnd)
withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) } if (on_message$silence) {{ invokeRestart("muffleMessage") } watcher$capture_plot_and_output()25: if (on_message$capture) {}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$push(cnd)eval(expr, envir) } if (on_message$silence) { invokeRestart("muffleMessage") if (on_warning$silence) { } invokeRestart("muffleWarning")}, warning = function (cnd)
watcher$capture_plot_and_output() if (on_warning$capture) { }26: }, error = function (cnd) {{ cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)withVisible(eval(expr, envir)) watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)
if (getOption("warn") >= 2 || getOption("warn") < 0) { return() watcher$push(cnd) } switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd) } if (on_warning$silence) {27: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})withCallingHandlers(code, error = function (e) invokeRestart("muffleWarning")})
}28: eval(call)
29: eval(call)
}, error = function (cnd) 28: 30: rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()with_handlers({ for (expr in tle$exprs) {eval(call) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE if (on_message$capture) {}, handlers)
{31: watcher$capture_plot_and_output() watcher$push(cnd)doWithOneRestart(return(expr), restart) cnd <- sanitize_call(cnd)
watcher$push(cnd)32: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: 29: eval(call)withOneRestart(expr, restarts[[1L]])eval(call)
}
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() if (on_message$silence) { watcher$print_value(ev$value, ev$visible, envir) }
invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) {33: TRUEwithRestartList(expr, restarts[-nr]) return()29: }
}, handlers)
watcher$capture_plot_and_output()31: 34: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
35: if (on_warning$capture) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
32: cnd <- sanitize_call(cnd)36: withRestartList(expr, restarts)eval(call)
30: with_handlers({ for (expr in tle$exprs) { watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning")37: withOneRestart(expr, restarts[[1L]])
ev <- withVisible(eval(expr, envir))33: watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr]) watcher$print_value(ev$value, ev$visible, envir) }withRestarts(with_handlers({
}}, error = function (cnd) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) TRUE34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
}, handlers){ watcher$capture_plot_and_output() watcher$capture_plot_and_output()36: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)31: })withRestartList(expr, restarts)doWithOneRestart(return(expr), restart)
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
28: eval(call)32:
29: 38: eval(call)
30: with_handlers({evaluate::evaluate(...)
37: for (expr in tle$exprs) {withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE
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$render, options))
40: in_dir(input_dir(), expr)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
withOneRestart(expr, restarts[[1L]])}, handlers)38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 31:
keep_message = if (is.numeric(options$message)) TRUE else options$message, 41: stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0LdoWithOneRestart(return(expr), restart)33: withRestartList(expr, restarts[-nr])in_input_dir(evaluate(code, envir = env, new_device = FALSE, else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 41:
34: keep_message = if (is.numeric(options$message)) TRUE else options$message, in_input_dir(evaluate(code, envir = env, new_device = FALSE, stop_on_error = if (is.numeric(options$error)) options$error else { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L stop_on_error = if (is.numeric(options$error)) options$error else {doWithOneRestart(return(expr), restart) if (options$error && options$include)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])32: 0L
else 2L36: withRestartList(expr, restarts) else 2L }, output_handler = knit_handlers(options$render, options)))withOneRestart(expr, restarts[[1L]])
37: withRestarts(with_handlers({
33: for (expr in tle$exprs) { }, output_handler = knit_handlers(options$render, options)))42:
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()eng_r(options)42:
watcher$print_value(ev$value, ev$visible, envir) }withRestartList(expr, restarts[-nr]) TRUE
34: doWithOneRestart(return(expr), restart)eng_r(options)
43: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])43: block_exec(params)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)44: call_block(x)block_exec(params)
36: 45: process_group(group)
46: withRestartList(expr, restarts)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 37:
withRestarts(with_handlers({38: for (expr in tle$exprs) { error = function(e) { 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: 44: evaluate::evaluate(...)call_block(x)
if (progress && is.function(pb$interrupt)) pb$interrupt()39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (is_R_CMD_build() || is_R_CMD_check()) keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
})45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (options$error && options$include) error = function(e) {
47: keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L stop_on_error = if (is.numeric(options$error)) options$error else { else 2L if (options$error && options$include) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: error = function(e) { 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
if (progress && is.function(pb$interrupt)) 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, in_input_dir(evaluate(code, envir = env, new_device = FALSE, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 0L keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) else 2L error <<- format(e) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())) if (options$error && options$include)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { }, output_handler = knit_handlers(options$render, options))) if (progress && is.function(pb$interrupt))
pb$interrupt() 0L else 2L42: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })eng_r(options)
43: 47: }, output_handler = knit_handlers(options$render, options)))
42: error <<- format(e)eng_r(options) }), list(rlang_trace_top_env = knit_global())), function(loc) {block_exec(params)
43:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 44: block_exec(params)call_block(x)
setwd(wd) write_utf8(res, output %n% stdout()) error = function(e) { paste0("\nQuitting from ", loc, if (!is.null(error)) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }), list(rlang_trace_top_env = knit_global()))
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44:
call_block(x)45:
48: 45: process_group(group)
process_group(group)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)46: 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {52: if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) vweave_rmarkdown(...) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))53: engine$weave(file, quiet = quiet, encoding = enc)
54: pb$interrupt()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
if (progress && is.function(pb$interrupt)) 49:
55: process_file(text, output)
50: tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt()56: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)tryCatchList(expr, classes, parentenv, handlers)
57: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) error <<- format(e)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { }), list(rlang_trace_top_env = knit_global()))51: texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...) engine = engine)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()) outputs <- c(outputs, output)
}, error = function(e) {53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", error <<- format(e) file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2XJpc5/file84a53549f681.rds")
tryCatchOne(expr, names, parentenv, handlers[[1L]])
47: An irrecoverable exception occurred. R is aborting now ...
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 56: tryCatchList(expr, classes, parentenv, handlers)
57: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(startdir) setwd(wd) write_utf8(res, output %n% stdout()) 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) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) } outputs <- c(outputs, output) write_utf8(res, output %n% stdout())}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
49: file, conditionMessage(e)))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(), ...)
paste0("\nQuitting from ", loc, if (!is.null(error)) 52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: paste0("\n", rule(), error, "\n", rule()))doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2XJpc5/file84a53549f681.rds")
output <- find_vignette_product(name, by = "weave", engine = engine)An irrecoverable exception occurred. R is aborting now ...
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: 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)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
}, 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/Rtmp2XJpc5/file84a53549f681.rds")
An irrecoverable exception occurred. R is aborting now ...
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2XJpc5/file84a53549f681.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