Last updated on 2026-10-12 07:52:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.49 | 219.56 | 223.05 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.74 | 229.12 | 231.86 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.60 | 213.69 | 217.29 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.18 | 212.69 | 215.87 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 5.00 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 35.00 | 37.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 157.00 | 165.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-10-12 16:38:12.295 R[44798:67370] XType: Using static font registry.
*** caught segfault ***
*** caught segfault ***
address 0x110, cause 'invalid permissions'
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
Traceback:
1: tau = tau, theta = th, exclusionRadius = exclusionRadius, RowCumsum(valid) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 4: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ComputeError(predictions$Observations, predictions$Predictions)
tieBreak = FALSE, verbose = verbose)
5: 3: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend) ignoreNan = ignoreNan, backend = backend)$predictions)
4:
ComputeError(predictions$Observations, predictions$Predictions) 6:
FUN(X[[i]], ...) 5:
7: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, lapply(X = S, FUN = FUN, ...) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 8: ignoreNan = ignoreNan, backend = backend)$predictions)doTryCatch(return(expr), name, parentenv, handler)
6: 9: FUN(X[[i]], ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: 10: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)
8: 11: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 9: if (!is.null(call)) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)10: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")tryCatchList(expr, classes, parentenv, handlers) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]11: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatch(expr, error = function(e) { if (is.na(w)) call <- conditionCall(e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (!is.null(call)) { type = "b") if (w > LONG) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste0(prefix, "\n ") call <- sys.call(-4L)
Traceback:
} 1: else prefix <- "Error : " dcall <- deparse(call, nlines = 1L)RowCumsum(valid) prefix <- paste("Error in", dcall, ": ")
msg <- paste0(prefix, conditionMessage(e), "\n") 2: .Internal(seterrmessage(msg[1L])) LONG <- 75L
Traceback:
sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (is.na(w)) 1: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, RowCumsum(valid) cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], .Internal(printDeferredWarnings()) type = "b") tieBreak = FALSE, verbose = verbose)
} if (w > LONG) invisible(structure(msg, class = "try-error", condition = e)) 2:
}) prefix <- paste0(prefix, "\n ")FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
3: }SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, else prefix <- "Error : " tau = tau, theta = th, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 12: tieBreak = FALSE, verbose = verbose)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) embedded = embedded, validLib = validLib, noTime = noTime, msg <- paste0(prefix, conditionMessage(e), "\n")
3: 13: .Internal(seterrmessage(msg[1L]))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (!silent && isTRUE(getOption("show.error.messages"))) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, ignoreNan = ignoreNan, backend = backend) tau = tau, theta = th, exclusionRadius = exclusionRadius, cat(msg, file = outFile) embedded = embedded, validLib = validLib, noTime = noTime,
.Internal(printDeferredWarnings())
14: } 4: FUN(X[[i]], ...) invisible(structure(msg, class = "try-error", condition = e))ComputeError(predictions$Observations, predictions$Predictions) ignoreNan = ignoreNan, backend = backend)
})15: 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 4: 12: embedded = embedded, validLib = validLib, noTime = noTime, ComputeError(predictions$Observations, predictions$Predictions)lapply(seq_len(cores), inner.do)
ignoreNan = ignoreNan, backend = backend)$predictions) 5: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 16:
embedded = embedded, validLib = validLib, noTime = noTime, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
ignoreNan = ignoreNan, backend = backend)$predictions)
6:
FUN(X[[i]], ...)13: 17: 6: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
7: 18: 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
lapply(X = S, FUN = FUN, ...)15:
lapply(seq_len(cores), inner.do)19: 8:
tryCatchList(expr, classes, parentenv, handlers) 8: doTryCatch(return(expr), name, parentenv, handler)16:
doTryCatch(return(expr), name, parentenv, handler)
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 9: 20: 9: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatchOne(expr, names, parentenv, handlers[[1L]]) mc.preschedule = TRUE), error = function(e) NULL)tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: 10: 17: tryCatchList(expr, classes, parentenv, handlers)21: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
11:
SweepApply(theta, worker, numProcess)tryCatch(expr, error = function(e) {11:
18: 22: call <- conditionCall(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {tryCatch(expr, error = function(e) {unlist(SweepApply(theta, worker, numProcess)) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)19: call <- conditionCall(e) dcall <- deparse(call, nlines = 1L)tryCatchList(expr, classes, parentenv, handlers) prefix <- paste("Error in", dcall, ": ")
if (!is.null(call)) {20: 23: if (identical(call[[1L]], quote(doTryCatch))) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, call <- sys.call(-4L) mc.preschedule = TRUE), error = function(e) NULL) LONG <- 75LPredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ")
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 21: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") LONG <- 75LSweepApply(theta, worker, numProcess) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is.na(w)) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], E = E, showPlot = TRUE)22:
if (is.na(w)) type = "b")unlist(SweepApply(theta, worker, numProcess)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
24: type = "b") if (w > LONG) eval(expr, envir) if (w > LONG) 23: prefix <- paste0(prefix, "\n ")
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", prefix <- paste0(prefix, "\n ")25: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", } E = E, showPlot = TRUE) else prefix <- "Error : "
eval(expr, envir) } msg <- paste0(prefix, conditionMessage(e), "\n")24:
else prefix <- "Error : "26: .Internal(seterrmessage(msg[1L])) msg <- paste0(prefix, conditionMessage(e), "\n")eval(expr, envir) if (!silent && isTRUE(getOption("show.error.messages"))) {
.Internal(seterrmessage(msg[1L])) cat(msg, file = outFile)25: withVisible(eval(expr, envir)) .Internal(printDeferredWarnings())
if (!silent && isTRUE(getOption("show.error.messages"))) {eval(expr, envir) }27: invisible(structure(msg, class = "try-error", condition = e)) cat(msg, file = outFile)
.Internal(printDeferredWarnings())})withCallingHandlers(code, error = function (e) }26: rlang::entrace(e), message = function (cnd) invisible(structure(msg, class = "try-error", condition = e))
})withVisible(eval(expr, envir))
12: 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE){
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)13: 27: watcher$capture_plot_and_output()
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))withCallingHandlers(code, error = function (e) if (on_message$capture) {rlang::entrace(e), message = function (cnd) 13: {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) watcher$capture_plot_and_output()
if (on_message$capture) {14: watcher$push(cnd) watcher$push(cnd) }FUN(X[[i]], ...)
14: if (on_message$silence) { }FUN(X[[i]], ...)15: invokeRestart("muffleMessage") if (on_message$silence) { }lapply(seq_len(cores), inner.do)}, warning = function (cnd) invokeRestart("muffleMessage")
{ } if (getOption("warn") >= 2 || getOption("warn") < 0) {16: }, warning = function (cnd) return(){ if (getOption("warn") >= 2 || getOption("warn") < 0) { }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$capture_plot_and_output()
if (on_warning$capture) {15: cnd <- sanitize_call(cnd) return() watcher$push(cnd)lapply(seq_len(cores), inner.do)17: }
if (on_warning$silence) { } invokeRestart("muffleWarning")16: } watcher$capture_plot_and_output()}, error = function (cnd) {doTryCatch(return(expr), name, parentenv, handler)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
if (on_warning$capture) {18: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) cnd <- sanitize_call(cnd)
cnd <- sanitize_call(cnd)
watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)19: }})17: if (on_warning$silence) {
invokeRestart("muffleWarning")doTryCatch(return(expr), name, parentenv, handler)28: }eval(call)tryCatchList(expr, classes, parentenv, handlers)
}, error = function (cnd)
29: {eval(call)
watcher$capture_plot_and_output()18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])20:
cnd <- sanitize_call(cnd)30: 19: with_handlers({ watcher$push(cnd)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, for (expr in tle$exprs) {tryCatchList(expr, classes, parentenv, handlers) mc.preschedule = TRUE), error = function(e) NULL) ev <- withVisible(eval(expr, envir)) switch(on_error, continue = invokeRestart("eval_continue"),
watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL)
})21: watcher$print_value(ev$value, ev$visible, envir)SweepApply(theta, worker, numProcess)
20:
28: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 22: mc.preschedule = TRUE), error = function(e) NULL)eval(call)
}21: unlist(SweepApply(theta, worker, numProcess)) TRUESweepApply(theta, worker, numProcess)
}, handlers)29: 22:
23: eval(call)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", unlist(SweepApply(theta, worker, numProcess))31: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", doWithOneRestart(return(expr), restart) E = E, showPlot = TRUE)
30: 24: 23: eval(expr, envir)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
with_handlers({32: 25: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", for (expr in tle$exprs) {withOneRestart(expr, restarts[[1L]]) E = E, showPlot = TRUE) ev <- withVisible(eval(expr, envir))eval(expr, envir)
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
33: 24: }eval(expr, envir)26: TRUE
}, handlers)withVisible(eval(expr, envir))25:
eval(expr, envir)31: withRestartList(expr, restarts[-nr])27:
withCallingHandlers(code, error = function (e)
doWithOneRestart(return(expr), restart)rlang::entrace(e), message = function (cnd) 26: {
34: watcher$capture_plot_and_output()withVisible(eval(expr, envir))doWithOneRestart(return(expr), restart)32: if (on_message$capture) {
withOneRestart(expr, restarts[[1L]]) watcher$push(cnd)
35: 33:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withRestartList(expr, restarts[-nr]) }27: if (on_message$silence) {
withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) invokeRestart("muffleMessage")36: {34: withRestartList(expr, restarts) }doWithOneRestart(return(expr), restart)
}, warning = function (cnd) 37: 35: { watcher$capture_plot_and_output()withRestarts(with_handlers({ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$capture) { for (expr in tle$exprs) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$push(cnd) ev <- withVisible(eval(expr, envir))
} watcher$capture_plot_and_output()36: return()withRestartList(expr, restarts) watcher$print_value(ev$value, ev$visible, envir) }
if (on_message$silence) {37: } watcher$capture_plot_and_output() invokeRestart("muffleMessage") TRUEwithRestarts(with_handlers({ if (on_warning$capture) { for (expr in tle$exprs) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) } ev <- withVisible(eval(expr, envir))
38: watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)evaluate::evaluate(...) watcher$print_value(ev$value, ev$visible, envir) watcher$push(cnd)}, warning = function (cnd) }{
TRUE } if (getOption("warn") >= 2 || getOption("warn") < 0) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)39: return()
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_warning$silence) { }38: invokeRestart("muffleWarning") watcher$capture_plot_and_output()evaluate::evaluate(...) keep_message = if (is.numeric(options$message)) TRUE else options$message, }
if (on_warning$capture) { stop_on_error = if (is.numeric(options$error)) options$error else { cnd <- sanitize_call(cnd) watcher$push(cnd) if (options$error && options$include) }}, error = function (cnd) 0L39: if (on_warning$silence) {{ else 2L invokeRestart("muffleWarning") }, output_handler = knit_handlers(options$render, options))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$capture_plot_and_output()
} cnd <- sanitize_call(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function (cnd) 40: stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd){ if (options$error && options$include) in_dir(input_dir(), expr) watcher$capture_plot_and_output() 0L cnd <- sanitize_call(cnd) switch(on_error, continue = invokeRestart("eval_continue"), else 2L stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), })41:
}, output_handler = knit_handlers(options$render, options)) stop = invokeRestart("eval_stop"), error = NULL)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 28: })eval(call) keep_message = if (is.numeric(options$message)) TRUE else options$message,
40: stop_on_error = if (is.numeric(options$error)) options$error else {in_dir(input_dir(), expr)
if (options$error && options$include) 28: 41: 29: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 0Leval(call)eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, else 2L
keep_message = if (is.numeric(options$message)) TRUE else options$message,
}, output_handler = knit_handlers(options$render, options)))29: stop_on_error = if (is.numeric(options$error)) options$error else {30:
eval(call)42:
with_handlers({ if (options$error && options$include) 30: eng_r(options) 0L for (expr in tle$exprs) {
43: with_handlers({ else 2Lblock_exec(params) ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) {
}, output_handler = knit_handlers(options$render, options)))44:
42: ev <- withVisible(eval(expr, envir))call_block(x)eng_r(options)
watcher$capture_plot_and_output()45: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
watcher$print_value(ev$value, ev$visible, envir) }process_group(group)43: }
TRUE TRUE}, handlers)}, handlers)46: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
44: error = function(e) {31: 31: call_block(x)doWithOneRestart(return(expr), restart) if (progress && is.function(pb$interrupt)) pb$interrupt()
doWithOneRestart(return(expr), restart)32: if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)withOneRestart(expr, restarts[[1L]])45: })
process_group(group)32: 33: 47:
withOneRestart(expr, restarts[[1L]])withRestartList(expr, restarts[-nr])46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
34: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 33: doWithOneRestart(return(expr), restart) error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt))
withRestartList(expr, restarts[-nr]) if (progress && is.function(pb$interrupt)) pb$interrupt()
pb$interrupt()35: if (is_R_CMD_build() || is_R_CMD_check()) 34: error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }), list(rlang_trace_top_env = knit_global())) error <<- format(e)doWithOneRestart(return(expr), restart)
})
35: 36: 48: withRestartList(expr, restarts)47: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {
36: error = function(e) {37: withRestartList(expr, restarts)withRestarts(with_handlers({ if (progress && is.function(pb$interrupt))
if (progress && is.function(pb$interrupt)) for (expr in tle$exprs) { pb$interrupt()37: ev <- withVisible(eval(expr, envir))withRestarts(with_handlers({ pb$interrupt() watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) for (expr in tle$exprs) { watcher$print_value(ev$value, ev$visible, envir) error <<- format(e) ev <- withVisible(eval(expr, envir)) } }), list(rlang_trace_top_env = knit_global())), function(loc) { TRUE if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) watcher$print_value(ev$value, ev$visible, envir) }), list(rlang_trace_top_env = knit_global()))}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
TRUE setwd(wd)
48: write_utf8(res, output %n% stdout())xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 38: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) paste0("\nQuitting from ", loc, if (!is.null(error)) error = function(e) {evaluate::evaluate(...)
paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (progress && is.function(pb$interrupt)) 38:
evaluate::evaluate(...)49:
pb$interrupt()process_file(text, output)39: 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())
error <<- format(e) keep_message = if (is.numeric(options$message)) TRUE else options$message, 50: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, stop_on_error = if (is.numeric(options$error)) options$error else { keep_message = if (is.numeric(options$message)) TRUE else options$message, }), list(rlang_trace_top_env = knit_global())), function(loc) { if (options$error && options$include) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) stop_on_error = if (is.numeric(options$error)) options$error else { setwd(wd) 0L
write_utf8(res, output %n% stdout()) if (options$error && options$include) 51: paste0("\nQuitting from ", loc, if (!is.null(error)) else 2Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 0L }, output_handler = knit_handlers(options$render, options)) paste0("\n", rule(), error, "\n", rule())) output_dir = getwd(), ...) else 2L
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
40:
}, output_handler = knit_handlers(options$render, options))in_dir(input_dir(), expr)
49:
52: process_file(text, output)41: vweave_rmarkdown(...)
40:
in_dir(input_dir(), expr)53:
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, engine$weave(file, quiet = quiet, encoding = enc)in_input_dir(evaluate(code, envir = env, new_device = FALSE, 50:
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 54: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)doTryCatch(return(expr), name, parentenv, handler) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), stop_on_error = if (is.numeric(options$error)) options$error else {55: if (options$error && options$include) if (options$error && options$include) output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L 0L else 2L
else 2L
}, output_handler = knit_handlers(options$render, options))) }, output_handler = knit_handlers(options$render, options)))56: 52:
tryCatchList(expr, classes, parentenv, handlers)
42: 42:
vweave_rmarkdown(...)eng_r(options)57: eng_r(options)
53:
43: engine$weave(file, quiet = quiet, encoding = enc)block_exec(params)
43: tryCatch({
54: block_exec(params) engine$weave(file, quiet = quiet, encoding = enc)
doTryCatch(return(expr), name, parentenv, handler) setwd(startdir)44:
output <- find_vignette_product(name, by = "weave", engine = engine)44: 55: call_block(x) if (!have.makefile && vignette_is_tex(output)) {tryCatchOne(expr, names, parentenv, handlers[[1L]])call_block(x) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
45: engine = engine)
process_group(group)56:
45: }46: process_group(group)tryCatchList(expr, classes, parentenv, handlers)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), outputs <- c(outputs, output) error = function(e) {
46: if (progress && is.function(pb$interrupt)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 57: }, error = function(e) {tryCatch({ error = function(e) { engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() thisOK <<- FALSE setwd(startdir) if (progress && is.function(pb$interrupt)) fails <<- c(fails, file) if (is_R_CMD_build() || is_R_CMD_check()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", pb$interrupt() output <- find_vignette_product(name, by = "weave", engine = engine) file, conditionMessage(e))) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) if (!have.makefile && vignette_is_tex(output)) { }) })
}) texi2pdf(file = output, clean = FALSE, quiet = quiet)
58: 47: output <- find_vignette_product(name, by = "texi2pdf", tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYkwKVi/file868879ea77be.rds")47: engine = engine)
} error = function(e) {An irrecoverable exception occurred. R is aborting now ...
outputs <- c(outputs, output) if (progress && is.function(pb$interrupt)) pb$interrupt()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { thisOK <<- FALSE error <<- format(e) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())) pb$interrupt() fails <<- c(fails, file)
if (is_R_CMD_build() || is_R_CMD_check()) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", error <<- format(e) file, conditionMessage(e)))48: })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global()))
error = function(e) {58: if (progress && is.function(pb$interrupt))
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYkwKVi/file868879ea77be.rds") error <<- format(e)48: }), list(rlang_trace_top_env = knit_global())), function(loc) {
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {An irrecoverable exception occurred. R is aborting now ...
setwd(wd) if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) paste0("\nQuitting from ", loc, if (!is.null(error)) 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())), function(loc) {
setwd(wd)49: write_utf8(res, output %n% stdout())process_file(text, output) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))50: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
49: 51: process_file(text, output)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)52:
51: vweave_rmarkdown(...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)53: engine$weave(file, quiet = quiet, encoding = enc)
52: 54: doTryCatch(return(expr), name, parentenv, handler)vweave_rmarkdown(...)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])53:
engine$weave(file, quiet = quiet, encoding = enc)56:
tryCatchList(expr, classes, parentenv, handlers)54:
doTryCatch(return(expr), name, parentenv, handler)57: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)55: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 56: engine = engine)tryCatchList(expr, classes, parentenv, handlers)
}57: outputs <- c(outputs, output)tryCatch({}, error = function(e) { engine$weave(file, quiet = quiet, encoding = enc) thisOK <<- FALSE setwd(startdir) fails <<- c(fails, file) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", output <- find_vignette_product(name, by = "texi2pdf", file, conditionMessage(e))) engine = engine)}) } outputs <- c(outputs, output)
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }, error = function(e) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpYkwKVi/file868879ea77be.rds") thisOK <<- FALSE
fails <<- c(fails, file)An irrecoverable exception occurred. R is aborting now ...
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/RtmpYkwKVi/file868879ea77be.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