Last updated on 2026-09-25 20:50:28 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.19 | 226.61 | 229.80 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.56 | 231.05 | 233.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.47 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.72 | 205.17 | 208.89 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.82 | 212.42 | 215.24 | 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 | 6.00 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 36.00 | 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 | 162.00 | 170.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-09-26 02:13:07.554 R[60017:91658] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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]], ...)
Traceback:
7: 1: lapply(X = S, FUN = FUN, ...)RowCumsum(valid)
8:
doTryCatch(return(expr), name, parentenv, handler) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
10: tieBreak = FALSE, verbose = verbose)tryCatchList(expr, classes, parentenv, handlers)
3: 11: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tryCatch(expr, error = function(e) { tau = tau, theta = th, exclusionRadius = exclusionRadius, call <- conditionCall(e) embedded = embedded, validLib = validLib, noTime = noTime, if (!is.null(call)) { ignoreNan = ignoreNan, backend = backend)
if (identical(call[[1L]], quote(doTryCatch))) 4: call <- sys.call(-4L)ComputeError(predictions$Observations, predictions$Predictions) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 5: sm <- strsplit(conditionMessage(e), "\n")[[1L]]SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (is.na(w)) embedded = embedded, validLib = validLib, noTime = noTime, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ignoreNan = ignoreNan, backend = backend)$predictions) type = "b")
if (w > LONG) 6: prefix <- paste0(prefix, "\n ") }FUN(X[[i]], ...) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 7: .Internal(seterrmessage(msg[1L]))lapply(X = S, FUN = FUN, ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 8: .Internal(printDeferredWarnings()) }doTryCatch(return(expr), name, parentenv, handler)
invisible(structure(msg, class = "try-error", condition = e)) 9: })tryCatchOne(expr, names, parentenv, handlers[[1L]])
12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
10: 13: tryCatchList(expr, classes, parentenv, handlers)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
11:
tryCatch(expr, error = function(e) {14: call <- conditionCall(e)FUN(X[[i]], ...)
if (!is.null(call)) {15: if (identical(call[[1L]], quote(doTryCatch))) lapply(seq_len(cores), inner.do) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L17: sm <- strsplit(conditionMessage(e), "\n")[[1L]]doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
18: if (is.na(w)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatchList(expr, classes, parentenv, handlers) type = "b")
if (w > LONG) 20: prefix <- paste0(prefix, "\n ")tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } mc.preschedule = TRUE), error = function(e) NULL) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")21: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {SweepApply(theta, worker, numProcess) cat(msg, file = outFile)
.Internal(printDeferredWarnings())22: }unlist(SweepApply(theta, worker, numProcess)) invisible(structure(msg, class = "try-error", condition = e))
})
12: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 13: E = E, showPlot = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24:
eval(expr, envir)
Traceback:
1: 25: 14: RowCumsum(valid)FUN(X[[i]], ...)
eval(expr, envir)
2: 15:
lapply(seq_len(cores), inner.do)26:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 16: withVisible(eval(expr, envir))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
17: 27: doTryCatch(return(expr), name, parentenv, handler) 3: withCallingHandlers(code, error = function (e)
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, rlang::entrace(e), message = function (cnd) 18: tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
{19: 4: watcher$capture_plot_and_output() if (on_message$capture) {ComputeError(predictions$Observations, predictions$Predictions)tryCatchList(expr, classes, parentenv, handlers)
watcher$push(cnd)20: 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, } knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, mc.preschedule = TRUE), error = function(e) NULL) if (on_message$silence) { embedded = embedded, validLib = validLib, noTime = noTime,
invokeRestart("muffleMessage") ignoreNan = ignoreNan, backend = backend)$predictions)21: }SweepApply(theta, worker, numProcess)
}, warning = function (cnd)
6: {FUN(X[[i]], ...)22:
if (getOption("warn") >= 2 || getOption("warn") < 0) {unlist(SweepApply(theta, worker, numProcess)) 7: return()lapply(X = S, FUN = FUN, ...)
23: }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 8: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
24: 9: eval(expr, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]])
if (on_warning$capture) {10: 25: tryCatchList(expr, classes, parentenv, handlers)
eval(expr, envir)11: tryCatch(expr, error = function(e) { cnd <- sanitize_call(cnd)
call <- conditionCall(e) watcher$push(cnd) if (!is.null(call)) {26: if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)withVisible(eval(expr, envir)) prefix <- paste("Error in", dcall, ": ")
if (on_warning$silence) {27: invokeRestart("muffleWarning")withCallingHandlers(code, error = function (e) } LONG <- 75Lrlang::entrace(e), message = function (cnd) sm <- strsplit(conditionMessage(e), "\n")[[1L]]}, error = function (cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w"){{ if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$capture_plot_and_output() watcher$capture_plot_and_output() type = "b") if (on_message$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) if (w > LONG) watcher$push(cnd) prefix <- paste0(prefix, "\n ") } } switch(on_error, continue = invokeRestart("eval_continue"), if (on_message$silence) { else prefix <- "Error : " stop = invokeRestart("eval_stop"), error = NULL) invokeRestart("muffleMessage") msg <- paste0(prefix, conditionMessage(e), "\n")}) } .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)}, warning = function (cnd) .Internal(printDeferredWarnings()){ }28: invisible(structure(msg, class = "try-error", condition = e)) if (getOption("warn") >= 2 || getOption("warn") < 0) {})eval(call)
12: return()try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
}29:
eval(call) watcher$capture_plot_and_output()13: if (on_warning$capture) {
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) cnd <- sanitize_call(cnd)
watcher$push(cnd)30: }14: if (on_warning$silence) {FUN(X[[i]], ...)with_handlers({ invokeRestart("muffleWarning")
} for (expr in tle$exprs) {15: }, error = function (cnd) ev <- withVisible(eval(expr, envir))lapply(seq_len(cores), inner.do)
watcher$capture_plot_and_output()16: { watcher$print_value(ev$value, ev$visible, envir)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd)
TRUE watcher$push(cnd)}, handlers) switch(on_error, continue = invokeRestart("eval_continue"), 17: stop = invokeRestart("eval_stop"), error = NULL)doTryCatch(return(expr), name, parentenv, handler)})
31: 28: doWithOneRestart(return(expr), restart)eval(call)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: 32: eval(call)withOneRestart(expr, restarts[[1L]])
Traceback:
33: 19: 1: tryCatchList(expr, classes, parentenv, handlers)
withRestartList(expr, restarts[-nr])RowCumsum(valid)
20: 34: 30:
doWithOneRestart(return(expr), restart)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 2: mc.preschedule = TRUE), error = function(e) NULL)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)21:
SweepApply(theta, worker, numProcess) 3: with_handlers({
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, for (expr in tle$exprs) {22: tau = tau, theta = th, exclusionRadius = exclusionRadius, unlist(SweepApply(theta, worker, numProcess))35:
ev <- withVisible(eval(expr, envir)) embedded = embedded, validLib = validLib, noTime = noTime, watcher$capture_plot_and_output()23: ignoreNan = ignoreNan, backend = backend)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$print_value(ev$value, ev$visible, envir) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", } E = E, showPlot = TRUE)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
TRUE
4: 36: }, handlers)withRestartList(expr, restarts)
31: 24: ComputeError(predictions$Observations, predictions$Predictions)37: eval(expr, envir)
5: doWithOneRestart(return(expr), restart)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, withRestarts(with_handlers({25:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, for (expr in tle$exprs) {32: embedded = embedded, validLib = validLib, noTime = noTime, ev <- withVisible(eval(expr, envir)) ignoreNan = ignoreNan, backend = backend)$predictions)withOneRestart(expr, restarts[[1L]])
eval(expr, envir) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)33: 6: }withRestartList(expr, restarts[-nr])FUN(X[[i]], ...)26:
withVisible(eval(expr, envir)) 7:
34: TRUElapply(X = S, FUN = FUN, ...)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
doWithOneRestart(return(expr), restart)
38: 8: 27: evaluate::evaluate(...)35:
doTryCatch(return(expr), name, parentenv, handler)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])39: withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 36: keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {{withRestartList(expr, restarts) if (options$error && options$include) 0L 9:
else 2LtryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options))
if (on_message$capture) {40: watcher$push(cnd)10: }tryCatchList(expr, classes, parentenv, handlers) if (on_message$silence) { invokeRestart("muffleMessage")
}11: 37: tryCatch(expr, error = function(e) {}, warning = function (cnd) {withRestarts(with_handlers({ call <- conditionCall(e) if (getOption("warn") >= 2 || getOption("warn") < 0) { for (expr in tle$exprs) { if (!is.null(call)) { ev <- withVisible(eval(expr, envir))in_dir(input_dir(), expr) return() if (identical(call[[1L]], quote(doTryCatch)))
watcher$capture_plot_and_output()41: call <- sys.call(-4L) }in_input_dir(evaluate(code, envir = env, new_device = FALSE, dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, LONG <- 75L watcher$print_value(ev$value, ev$visible, envir) sm <- strsplit(conditionMessage(e), "\n")[[1L]] keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_warning$capture) { if (is.na(w)) } cnd <- sanitize_call(cnd) TRUE watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (options$error && options$include) type = "b") 0L } else 2L
if (on_warning$silence) { if (w > LONG) invokeRestart("muffleWarning")38: prefix <- paste0(prefix, "\n ") }, output_handler = knit_handlers(options$render, options))) }
else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n")evaluate::evaluate(...)42:
}, error = function (cnd) eng_r(options)39:
.Internal(seterrmessage(msg[1L])){ if (!silent && isTRUE(getOption("show.error.messages"))) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 43: cat(msg, file = outFile) watcher$capture_plot_and_output()block_exec(params) keep_message = if (is.numeric(options$message)) TRUE else options$message, .Internal(printDeferredWarnings()) cnd <- sanitize_call(cnd)
stop_on_error = if (is.numeric(options$error)) options$error else {44: }call_block(x) if (options$error && options$include)
watcher$push(cnd) invisible(structure(msg, class = "try-error", condition = e))45: 0L switch(on_error, continue = invokeRestart("eval_continue"), process_group(group) stop = invokeRestart("eval_stop"), error = NULL)}) else 2L})
}, output_handler = knit_handlers(options$render, options))
40: 46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), in_dir(input_dir(), expr) error = function(e) {
if (progress && is.function(pb$interrupt)) 41: 28: pb$interrupt()12: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)eval(call)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
})29:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
13: 47: keep_message = if (is.numeric(options$message)) TRUE else options$message, with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) error = function(e) {
stop_on_error = if (is.numeric(options$error)) options$error else {30:
if (options$error && options$include) 14: with_handlers({FUN(X[[i]], ...) 0L for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output()15: watcher$print_value(ev$value, ev$visible, envir)lapply(seq_len(cores), inner.do) else 2L pb$interrupt()
} }, output_handler = knit_handlers(options$render, options))) if (is_R_CMD_build() || is_R_CMD_check()) 16: TRUE
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) error <<- format(e)}, handlers) }), list(rlang_trace_top_env = knit_global()))42:
eng_r(options)17: 48: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])31: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
doWithOneRestart(return(expr), restart) error = function(e) {19: 43:
tryCatchList(expr, classes, parentenv, handlers)block_exec(params) if (progress && is.function(pb$interrupt))
32: 20: withOneRestart(expr, restarts[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores, pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 33: 44: error <<- format(e) mc.preschedule = TRUE), error = function(e) NULL)withRestartList(expr, restarts[-nr])
call_block(x)34: }), list(rlang_trace_top_env = knit_global())), function(loc) {
doWithOneRestart(return(expr), restart)21: setwd(wd)
SweepApply(theta, worker, numProcess)
45: write_utf8(res, output %n% stdout())
35: process_group(group)22:
unlist(SweepApply(theta, worker, numProcess))
paste0("\nQuitting from ", loc, if (!is.null(error)) 23: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", paste0("\n", rule(), error, "\n", rule())) E = E, showPlot = TRUE)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)36:
49: 46: process_file(text, output)withRestartList(expr, restarts)24:
eval(expr, envir)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
37: error = function(e) {withRestarts(with_handlers({ if (progress && is.function(pb$interrupt)) 25: 50: eval(expr, envir) for (expr in tle$exprs) { pb$interrupt() ev <- withVisible(eval(expr, envir)) if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
watcher$print_value(ev$value, ev$visible, envir)
}26: error <<- format(e) TRUE51: withVisible(eval(expr, envir)) })rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
output_dir = getwd(), ...)
27:
47: withCallingHandlers(code, error = function (e) 52: rlang::entrace(e), message = function (cnd) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), vweave_rmarkdown(...) error = function(e) {
53: {engine$weave(file, quiet = quiet, encoding = enc) watcher$capture_plot_and_output()38: if (on_message$capture) {
watcher$push(cnd) if (progress && is.function(pb$interrupt)) } pb$interrupt()54: evaluate::evaluate(...) if (on_message$silence) {doTryCatch(return(expr), name, parentenv, handler) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) invokeRestart("muffleMessage")55: }), list(rlang_trace_top_env = knit_global())) }tryCatchOne(expr, names, parentenv, handlers[[1L]])39:
56: }, warning = function (cnd) evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatchList(expr, classes, parentenv, handlers)
{ keep_message = if (is.numeric(options$message)) TRUE else options$message, if (getOption("warn") >= 2 || getOption("warn") < 0) {48: stop_on_error = if (is.numeric(options$error)) options$error else {
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), return() if (options$error && options$include) 57: error = function(e) { } 0LtryCatch({ watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() setwd(startdir) if (is_R_CMD_build() || is_R_CMD_check()) else 2L if (on_warning$capture) { }, output_handler = knit_handlers(options$render, options)) output <- find_vignette_product(name, by = "weave", engine = engine) error <<- format(e)
if (!have.makefile && vignette_is_tex(output)) { }), list(rlang_trace_top_env = knit_global())), function(loc) { texi2pdf(file = output, clean = FALSE, quiet = quiet) cnd <- sanitize_call(cnd)40: watcher$push(cnd) output <- find_vignette_product(name, by = "texi2pdf", in_dir(input_dir(), expr) engine = engine) } } setwd(wd) outputs <- c(outputs, output)
}, error = function(e) { write_utf8(res, output %n% stdout()) thisOK <<- FALSE paste0("\nQuitting from ", loc, if (!is.null(error)) if (on_warning$silence) { paste0("\n", rule(), error, "\n", rule()))41: fails <<- c(fails, file) invokeRestart("muffleWarning")in_input_dir(evaluate(code, envir = env, new_device = FALSE, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, file, conditionMessage(e))) keep_message = if (is.numeric(options$message)) TRUE else options$message,
}) stop_on_error = if (is.numeric(options$error)) options$error else {}, error = function (cnd) if (options$error && options$include)
49: 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmposBDNU/filead575cb6c479.rds")process_file(text, output)
0LAn irrecoverable exception occurred. R is aborting now ...
else 2L50: }, output_handler = knit_handlers(options$render, options)))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
42: watcher$capture_plot_and_output()51: cnd <- sanitize_call(cnd)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), eng_r(options) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
output_dir = getwd(), ...) stop = invokeRestart("eval_stop"), error = NULL)
})43: 52:
vweave_rmarkdown(...)
block_exec(params)53:
engine$weave(file, quiet = quiet, encoding = enc)44:
call_block(x)54: 28: doTryCatch(return(expr), name, parentenv, handler)
eval(call)
55: 29: 45: eval(call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
process_group(group)30: 56: with_handlers({tryCatchList(expr, classes, parentenv, handlers)
for (expr in tle$exprs) {
46: 57: ev <- withVisible(eval(expr, envir))withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() error = function(e) {tryCatch({ if (progress && is.function(pb$interrupt)) engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() watcher$print_value(ev$value, ev$visible, envir) setwd(startdir) } output <- find_vignette_product(name, by = "weave", engine = engine) TRUE}, handlers) if (is_R_CMD_build() || is_R_CMD_check())
31: error <<- format(e)doWithOneRestart(return(expr), restart)
if (!have.makefile && vignette_is_tex(output)) { })32: texi2pdf(file = output, clean = FALSE, quiet = quiet)withOneRestart(expr, restarts[[1L]])
33: output <- find_vignette_product(name, by = "texi2pdf", withRestartList(expr, restarts[-nr]) engine = engine)
}47: outputs <- c(outputs, output)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function(e) { error = function(e) { thisOK <<- FALSE
if (progress && is.function(pb$interrupt)) 34: fails <<- c(fails, file)doWithOneRestart(return(expr), restart) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", pb$interrupt() file, conditionMessage(e)))
if (is_R_CMD_build() || is_R_CMD_check()) }) error <<- format(e)
35: 58: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", }), list(rlang_trace_top_env = knit_global()))
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmposBDNU/filead575cb6c479.rds")48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), An irrecoverable exception occurred. R is aborting now ...
error = function(e) {36: if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts) pb$interrupt()
37: if (is_R_CMD_build() || is_R_CMD_check()) withRestarts(with_handlers({ for (expr in tle$exprs) { error <<- format(e) ev <- withVisible(eval(expr, envir)) }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$capture_plot_and_output() setwd(wd) watcher$print_value(ev$value, ev$visible, envir) } write_utf8(res, output %n% stdout()) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: 38: evaluate::evaluate(...)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
39: 51: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { output_dir = getwd(), ...)
if (options$error && options$include) 52: 0Lvweave_rmarkdown(...) else 2L
}, output_handler = knit_handlers(options$render, options))53: engine$weave(file, quiet = quiet, encoding = enc)
40: 54: doTryCatch(return(expr), name, parentenv, handler)in_dir(input_dir(), expr)
55: 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 56: keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 57: 0LtryCatch({ else 2L }, output_handler = knit_handlers(options$render, options)))
engine$weave(file, quiet = quiet, encoding = enc)42: setwd(startdir)eng_r(options) 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", 43: engine = engine)block_exec(params) }
44: call_block(x)
outputs <- c(outputs, output)45: }, error = function(e) {process_group(group) thisOK <<- FALSE
fails <<- c(fails, file)46: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), file, conditionMessage(e))) error = function(e) {}) if (progress && is.function(pb$interrupt))
pb$interrupt()58: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", })
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmposBDNU/filead575cb6c479.rds")
47: An irrecoverable exception occurred. R is aborting now ...
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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/RtmposBDNU/filead575cb6c479.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