Last updated on 2026-11-15 07:50:57 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.68 | 225.13 | 228.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.66 | 231.27 | 233.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 174.74 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.27 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.32 | 208.12 | 212.44 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.89 | 214.98 | 217.87 | 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 | 4.00 | 131.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 43.00 | 45.00 | 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 | 156.00 | 164.00 | 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
2026-11-15 14:17:51.224 R[42417:64661] XType: Using static font registry.
*** 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3:
*** caught segfault ***
address 0x110, cause 'invalid permissions'
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
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") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26:
*** caught segfault ***
address 0x110, cause 'invalid permissions'
withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
Traceback:
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) 1: output <- find_vignette_product(name, by = "texi2pdf", RowCumsum(valid) engine = engine)
} outputs <- c(outputs, output) 2: }, error = function(e) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, thisOK <<- FALSE tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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:
1: RowCumsum(valid)
2: fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, file, conditionMessage(e))) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }) tieBreak = FALSE, verbose = verbose)
58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 3: 7: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpCVpE8U/file90fb3aa0f9da.rds")lapply(X = S, FUN = FUN, ...)
8: An irrecoverable exception occurred. R is aborting now ...
doTryCatch(return(expr), name, parentenv, handler)
tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 9: ignoreNan = ignoreNan, backend = backend)tryCatchOne(expr, names, parentenv, handlers[[1L]])
4:
ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 10: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
tryCatchList(expr, classes, parentenv, handlers)
6: 11: FUN(X[[i]], ...)
tryCatch(expr, error = function(e) { 7: call <- conditionCall(e)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 8: doTryCatch(return(expr), name, parentenv, handler)
sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 9: if (is.na(w)) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")tryCatchList(expr, classes, parentenv, handlers) if (w > LONG)
prefix <- paste0(prefix, "\n ")11: tryCatch(expr, error = function(e) { } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") call <- conditionCall(e) .Internal(seterrmessage(msg[1L])) if (!is.null(call)) { if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) if (identical(call[[1L]], quote(doTryCatch))) .Internal(printDeferredWarnings()) call <- sys.call(-4L) } invisible(structure(msg, class = "try-error", condition = e)) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], FUN(X[[i]], ...)
type = "b")15: lapply(seq_len(cores), inner.do) if (w > LONG)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) prefix <- paste0(prefix, "\n ") }
17: doTryCatch(return(expr), name, parentenv, handler) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
.Internal(seterrmessage(msg[1L]))19: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchList(expr, classes, parentenv, handlers)
20: cat(msg, file = outFile)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, .Internal(printDeferredWarnings()) mc.preschedule = TRUE), error = function(e) NULL) }
invisible(structure(msg, class = "try-error", condition = e))21: })SweepApply(theta, worker, numProcess)
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
22: unlist(SweepApply(theta, worker, numProcess))13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 14: FUN(X[[i]], ...) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
15:
lapply(seq_len(cores), inner.do)24: eval(expr, envir)
25: eval(expr, envir)
16: 26: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withVisible(eval(expr, envir))
27: 17: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
if (on_message$capture) { watcher$push(cnd)18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers) } if (on_message$silence) {
invokeRestart("muffleMessage")20: }tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)}, warning = function (cnd)
{21: if (getOption("warn") >= 2 || getOption("warn") < 0) { return()SweepApply(theta, worker, numProcess)
}22: watcher$capture_plot_and_output() if (on_warning$capture) {unlist(SweepApply(theta, worker, numProcess)) cnd <- sanitize_call(cnd)
23: watcher$push(cnd) }PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (on_warning$silence) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", invokeRestart("muffleWarning") E = E, showPlot = TRUE) }
24: eval(expr, envir)}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()25: watcher$print_value(ev$value, ev$visible, envir)eval(expr, envir)
26: withVisible(eval(expr, envir)) }
TRUE27: }, handlers)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) {31: watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) }doWithOneRestart(return(expr), restart) if (on_message$silence) {
32: withOneRestart(expr, restarts[[1L]]) invokeRestart("muffleMessage")
}33: }, warning = function (cnd) withRestartList(expr, restarts[-nr]){
if (getOption("warn") >= 2 || getOption("warn") < 0) {34: return()doWithOneRestart(return(expr), restart) } watcher$capture_plot_and_output() if (on_warning$capture) {
cnd <- sanitize_call(cnd)35: watcher$push(cnd) }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
if (on_warning$silence) {36: invokeRestart("muffleWarning") }withRestartList(expr, restarts)}, error = function (cnd) { watcher$capture_plot_and_output()
37: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)withRestarts(with_handlers({}) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))28:
Traceback:
watcher$capture_plot_and_output()eval(call) watcher$print_value(ev$value, ev$visible, envir) 1:
RowCumsum(valid) }29:
2: TRUEFindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, eval(call) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) tieBreak = FALSE, verbose = verbose)30:
with_handlers({38:
3: evaluate::evaluate(...) for (expr in tle$exprs) {
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 39: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { watcher$print_value(ev$value, ev$visible, envir) tau = tau, theta = th, exclusionRadius = exclusionRadius, if (options$error && options$include) } embedded = embedded, validLib = validLib, noTime = noTime, TRUE 0L}, handlers) ignoreNan = ignoreNan, backend = backend)
else 2L
}, output_handler = knit_handlers(options$render, options))31:
40: in_dir(input_dir(), expr)doWithOneRestart(return(expr), restart)
4: 41: 32: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, ComputeError(predictions$Observations, predictions$Predictions) keep_message = if (is.numeric(options$message)) TRUE else options$message, withOneRestart(expr, restarts[[1L]])
stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 5: 0L
else 2LSweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, }, output_handler = knit_handlers(options$render, options)))33:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 42: eng_r(options) embedded = embedded, validLib = validLib, noTime = noTime, withRestartList(expr, restarts[-nr])
ignoreNan = ignoreNan, backend = backend)$predictions)
43: 34:
6: block_exec(params)doWithOneRestart(return(expr), restart)
44: 35: call_block(x)FUN(X[[i]], ...)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 7: 45: lapply(X = S, FUN = FUN, ...)process_group(group)
36:
46: withRestartList(expr, restarts)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 8: error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 37: 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestarts(with_handlers({ error <<- format(e) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
})10: watcher$capture_plot_and_output()tryCatchList(expr, classes, parentenv, handlers)
watcher$print_value(ev$value, ev$visible, envir)
}47: 11: TRUEwith_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) error = function(e) {tryCatch(expr, error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 38: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))evaluate::evaluate(...)
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) error = function(e) { call <- sys.call(-4L) if (progress && is.function(pb$interrupt)) dcall <- deparse(call, nlines = 1L)
pb$interrupt()39: prefix <- paste("Error in", dcall, ": ") if (is_R_CMD_build() || is_R_CMD_check()) LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") keep_message = if (is.numeric(options$message)) TRUE else options$message, error <<- format(e) if (is.na(w)) stop_on_error = if (is.numeric(options$error)) options$error else { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } if (options$error && options$include) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) 0L else 2L }), 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)) }, output_handler = knit_handlers(options$render, options)) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }40:
in_dir(input_dir(), expr)49:
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, process_file(text, output) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {50: if (options$error && options$include) 0L invisible(structure(msg, class = "try-error", condition = e)) else 2Lknitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }, output_handler = knit_handlers(options$render, options)))
42: })
12: 51: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)eng_r(options)
13: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))43:
14: block_exec(params) output_dir = getwd(), ...)FUN(X[[i]], ...)
15: 52: lapply(seq_len(cores), inner.do)
vweave_rmarkdown(...)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)44: call_block(x)
20: 45: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, process_group(group) mc.preschedule = TRUE), error = function(e) NULL)
21:
46: 53: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()engine$weave(file, quiet = quiet, encoding = enc)
if (is_R_CMD_build() || is_R_CMD_check()) SweepApply(theta, worker, numProcess) error <<- format(e) })54:
doTryCatch(return(expr), name, parentenv, handler)22:
47: 55: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchOne(expr, names, parentenv, handlers[[1L]]) error = function(e) {
if (progress && is.function(pb$interrupt)) 56: unlist(SweepApply(theta, worker, numProcess))tryCatchList(expr, classes, parentenv, handlers) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", error <<- format(e) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) }), list(rlang_trace_top_env = knit_global()))
24: 48: eval(expr, envir)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
25: error = function(e) {eval(expr, envir)
26: if (progress && is.function(pb$interrupt)) withVisible(eval(expr, envir)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {57: setwd(wd)tryCatch({ write_utf8(res, output %n% stdout())
27: paste0("\nQuitting from ", loc, if (!is.null(error)) withCallingHandlers(code, error = function (e) engine$weave(file, quiet = quiet, encoding = enc)rlang::entrace(e), message = function (cnd) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc){ watcher$capture_plot_and_output() setwd(startdir)
if (on_message$capture) {49: output <- find_vignette_product(name, by = "weave", engine = engine) watcher$push(cnd)process_file(text, output) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) }
output <- find_vignette_product(name, by = "texi2pdf", if (on_message$silence) {50: invokeRestart("muffleMessage")knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
engine = engine)}, warning = function (cnd) 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), { } if (getOption("warn") >= 2 || getOption("warn") < 0) { output_dir = getwd(), ...) return()
outputs <- c(outputs, output)}, error = function(e) {52: thisOK <<- FALSE } fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))vweave_rmarkdown(...) watcher$capture_plot_and_output()
})53: if (on_warning$capture) {engine$weave(file, quiet = quiet, encoding = enc) cnd <- sanitize_call(cnd) watcher$push(cnd)
} if (on_warning$silence) {54: 58: invokeRestart("muffleWarning")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", doTryCatch(return(expr), name, parentenv, handler) } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpCVpE8U/file90fb3aa0f9da.rds")
55:
}, error = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]])An irrecoverable exception occurred. R is aborting now ...
{
56: watcher$capture_plot_and_output()tryCatchList(expr, classes, parentenv, handlers) cnd <- sanitize_call(cnd)
watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), 57: tryCatch({ stop = invokeRestart("eval_stop"), error = NULL)}) engine$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", 28: eval(call)
engine = engine) }29: outputs <- c(outputs, output)eval(call)}, error = function(e) {
thisOK <<- FALSE30: fails <<- c(fails, file)with_handlers({ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", for (expr in tle$exprs) { file, conditionMessage(e))) ev <- withVisible(eval(expr, envir))})
watcher$capture_plot_and_output()58: watcher$print_value(ev$value, ev$visible, envir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpCVpE8U/file90fb3aa0f9da.rds") TRUE
}, handlers)An irrecoverable exception occurred. R is aborting now ...
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: call_block(x)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() 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/RtmpCVpE8U/file90fb3aa0f9da.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