Last updated on 2026-10-23 17:52:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.91 | 223.80 | 227.71 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.48 | 245.41 | 247.89 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 169.42 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 191.21 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 139.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.75 | 212.15 | 215.90 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.20 | 209.21 | 212.41 | 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 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 46.00 | 48.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 164.00 | 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
2026-10-24 01:32:14.463 R[49957:73787] 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)
Traceback:
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 1: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, RowCumsum(valid) tieBreak = FALSE, verbose = verbose)
2: 3: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tau = tau, theta = th, exclusionRadius = exclusionRadius, tieBreak = FALSE, verbose = verbose)
embedded = embedded, validLib = validLib, noTime = noTime, 3: ignoreNan = ignoreNan, backend = backend)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 4: embedded = embedded, validLib = validLib, noTime = noTime, ComputeError(predictions$Observations, predictions$Predictions)
ignoreNan = ignoreNan, backend = backend) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 4: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ComputeError(predictions$Observations, predictions$Predictions) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 6: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, FUN(X[[i]], ...) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions) 7:
lapply(X = S, FUN = FUN, ...) 6:
FUN(X[[i]], ...) 8:
doTryCatch(return(expr), name, parentenv, handler) 7:
lapply(X = S, FUN = FUN, ...) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8:
doTryCatch(return(expr), name, parentenv, handler)10: tryCatchList(expr, classes, parentenv, handlers)
9:
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(expr, error = function(e) {
call <- conditionCall(e)10: if (!is.null(call)) {tryCatchList(expr, classes, parentenv, handlers) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)11: dcall <- deparse(call, nlines = 1L)tryCatch(expr, error = function(e) { prefix <- paste("Error in", dcall, ": ") call <- conditionCall(e) LONG <- 75L if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") dcall <- deparse(call, nlines = 1L) if (is.na(w)) prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], LONG <- 75L type = "b") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (w > LONG) prefix <- paste0(prefix, "\n ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) else prefix <- "Error : " w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") msg <- paste0(prefix, conditionMessage(e), "\n") if (w > LONG) .Internal(seterrmessage(msg[1L])) prefix <- paste0(prefix, "\n ") if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) else prefix <- "Error : " .Internal(printDeferredWarnings()) msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) invisible(structure(msg, class = "try-error", condition = e)) if (!silent && isTRUE(getOption("show.error.messages"))) {}) cat(msg, file = outFile)
.Internal(printDeferredWarnings())12: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invisible(structure(msg, class = "try-error", condition = e))
})13:
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
14: 15: lapply(seq_len(cores), inner.do)FUN(X[[i]], ...)
16:
15: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)lapply(seq_len(cores), inner.do)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])16:
19: tryCatchList(expr, classes, parentenv, handlers)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 17: mc.preschedule = TRUE), error = function(e) NULL)doTryCatch(return(expr), name, parentenv, handler)
21: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepApply(theta, worker, numProcess)
22: 19: unlist(SweepApply(theta, worker, numProcess))tryCatchList(expr, classes, parentenv, handlers)
20: 23: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", mc.preschedule = TRUE), error = function(e) NULL) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
21: E = E, showPlot = TRUE)SweepApply(theta, worker, numProcess)
22: 24: eval(expr, envir)unlist(SweepApply(theta, worker, numProcess))
25: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", eval(expr, envir) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)
26: 24: withVisible(eval(expr, envir))eval(expr, envir)
27: 25: withCallingHandlers(code, error = function (e) eval(expr, envir)rlang::entrace(e), message = function (cnd) {
watcher$capture_plot_and_output()26: if (on_message$capture) {withVisible(eval(expr, envir)) watcher$push(cnd)
}27: withCallingHandlers(code, error = function (e) if (on_message$silence) { invokeRestart("muffleMessage")rlang::entrace(e), message = function (cnd) }{}, warning = function (cnd) watcher$capture_plot_and_output(){ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$capture) { return() watcher$push(cnd) } } if (on_message$silence) { watcher$capture_plot_and_output() invokeRestart("muffleMessage") if (on_warning$capture) { } cnd <- sanitize_call(cnd) watcher$push(cnd)}, warning = function (cnd) }{ if (on_warning$silence) { if (getOption("warn") >= 2 || getOption("warn") < 0) { invokeRestart("muffleWarning") return() } }}, error = function (cnd) { watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) cnd <- sanitize_call(cnd) switch(on_error, continue = invokeRestart("eval_continue"), watcher$push(cnd) stop = invokeRestart("eval_stop"), error = NULL) }}) if (on_warning$silence) {
invokeRestart("muffleWarning")28: }eval(call)}, error = function (cnd)
{29: watcher$capture_plot_and_output()eval(call)
cnd <- sanitize_call(cnd) watcher$push(cnd)30: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)with_handlers({ for (expr in tle$exprs) {})
ev <- withVisible(eval(expr, envir))28: watcher$capture_plot_and_output()eval(call) watcher$print_value(ev$value, ev$visible, envir)
}29: TRUEeval(call)
}, handlers)30: with_handlers({
for (expr in tle$exprs) {31: doWithOneRestart(return(expr), restart) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()32: watcher$print_value(ev$value, ev$visible, envir)withOneRestart(expr, restarts[[1L]])
}33: withRestartList(expr, restarts[-nr])
TRUE34: }, handlers)doWithOneRestart(return(expr), restart)
35: 31: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])doWithOneRestart(return(expr), restart)
36: 32: withRestartList(expr, restarts)withOneRestart(expr, restarts[[1L]])
37: withRestarts(with_handlers({33: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withRestartList(expr, restarts[-nr]) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)34: }doWithOneRestart(return(expr), restart) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])38: evaluate::evaluate(...)
36: 39: withRestartList(expr, restarts)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {withRestarts(with_handlers({ if (options$error && options$include) for (expr in tle$exprs) { 0L ev <- withVisible(eval(expr, envir)) else 2L }, output_handler = knit_handlers(options$render, options)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)40: }in_dir(input_dir(), expr) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 38: keep_message = if (is.numeric(options$message)) TRUE else options$message, evaluate::evaluate(...) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 39:
Traceback:
0L 1: else 2Levaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, output_handler = knit_handlers(options$render, options)))RowCumsum(valid) keep_message = if (is.numeric(options$message)) TRUE else options$message,
42: stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) eng_r(options) 2:
0LFindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 43: else 2L validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }, output_handler = knit_handlers(options$render, options)) tieBreak = FALSE, verbose = verbose)block_exec(params)
3: 44: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
call_block(x) tau = tau, theta = th, exclusionRadius = exclusionRadius, 40:
embedded = embedded, validLib = validLib, noTime = noTime, in_dir(input_dir(), expr) ignoreNan = ignoreNan, backend = backend)
45: 4: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, ComputeError(predictions$Observations, predictions$Predictions) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
process_group(group) 5:
46: keep_message = if (is.numeric(options$message)) TRUE else options$message, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, error = function(e) { stop_on_error = if (is.numeric(options$error)) options$error else { if (progress && is.function(pb$interrupt)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (options$error && options$include) embedded = embedded, validLib = validLib, noTime = noTime, 0L pb$interrupt() else 2L ignoreNan = ignoreNan, backend = backend)$predictions) }, output_handler = knit_handlers(options$render, options)))
if (is_R_CMD_build() || is_R_CMD_check()) 42: error <<- format(e) 6: eng_r(options)FUN(X[[i]], ...)
})
43: 7: 47: block_exec(params)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
lapply(X = S, FUN = FUN, ...) error = function(e) {44:
if (progress && is.function(pb$interrupt)) call_block(x) 8: doTryCatch(return(expr), name, parentenv, handler) pb$interrupt()
9: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])process_group(group) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)10: 46: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global()))11:
tryCatch(expr, error = function(e) { pb$interrupt()48: if (is_R_CMD_build() || is_R_CMD_check()) call <- conditionCall(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) error = function(e) { if (!is.null(call)) { }) if (identical(call[[1L]], quote(doTryCatch))) if (progress && is.function(pb$interrupt))
pb$interrupt()47: call <- sys.call(-4L) if (is_R_CMD_build() || is_R_CMD_check()) dcall <- deparse(call, nlines = 1L)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) prefix <- paste("Error in", dcall, ": ") error = function(e) { }), list(rlang_trace_top_env = knit_global())), function(loc) { LONG <- 75L setwd(wd) if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) pb$interrupt() sm <- strsplit(conditionMessage(e), "\n")[[1L]] 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())) }), list(rlang_trace_top_env = knit_global()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) 48: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
49: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {process_file(text, output) if (progress && is.function(pb$interrupt)) pb$interrupt() type = "b")
if (is_R_CMD_build() || is_R_CMD_check()) if (w > LONG) error <<- format(e)50: prefix <- paste0(prefix, "\n ") }), list(rlang_trace_top_env = knit_global())), function(loc) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 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) }
51: else prefix <- "Error : "49: msg <- paste0(prefix, conditionMessage(e), "\n")process_file(text, output)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), .Internal(seterrmessage(msg[1L]))
output_dir = getwd(), ...)
if (!silent && isTRUE(getOption("show.error.messages"))) {52: cat(msg, file = outFile)50: vweave_rmarkdown(...)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
.Internal(printDeferredWarnings())
}53: invisible(structure(msg, class = "try-error", condition = e))})engine$weave(file, quiet = quiet, encoding = enc)51:
54: 12: doTryCatch(return(expr), name, parentenv, handler)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
55: output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
56:
tryCatchList(expr, classes, parentenv, handlers)
57: 13: tryCatch({sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) engine$weave(file, quiet = quiet, encoding = enc)52:
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)14: if (!have.makefile && vignette_is_tex(output)) {FUN(X[[i]], ...)
vweave_rmarkdown(...)15: texi2pdf(file = output, clean = FALSE, quiet = quiet)lapply(seq_len(cores), inner.do) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)53: }
engine$weave(file, quiet = quiet, encoding = enc) outputs <- c(outputs, output)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)}, error = function(e) {54:
thisOK <<- FALSE17: fails <<- c(fails, file)doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
18: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))tryCatchOne(expr, names, parentenv, handlers[[1L]])})
Traceback:
55: 58: 1: tryCatchOne(expr, names, parentenv, handlers[[1L]])RowCumsum(valid)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWogLws/file8a582415a0a7.rds")
19: 56:
2: tryCatchList(expr, classes, parentenv, handlers)An irrecoverable exception occurred. R is aborting now ...
tryCatchList(expr, classes, parentenv, handlers)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 57: 20: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatch({ mc.preschedule = TRUE), error = function(e) NULL) tieBreak = FALSE, verbose = verbose) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) 3:
output <- find_vignette_product(name, by = "weave", engine = engine)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)21: tau = tau, theta = th, exclusionRadius = exclusionRadius, output <- find_vignette_product(name, by = "texi2pdf", SweepApply(theta, worker, numProcess) embedded = embedded, validLib = validLib, noTime = noTime, engine = engine) ignoreNan = ignoreNan, backend = backend)
22: }unlist(SweepApply(theta, worker, numProcess)) 4: outputs <- c(outputs, output)
ComputeError(predictions$Observations, predictions$Predictions)23: }, error = function(e) {
thisOK <<- FALSE 5: fails <<- c(fails, file)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, E = E, showPlot = TRUE)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 24: embedded = embedded, validLib = validLib, noTime = noTime, file, conditionMessage(e))) ignoreNan = ignoreNan, backend = backend)$predictions)eval(expr, envir)
})25: 6:
FUN(X[[i]], ...)58:
eval(expr, envir) 7: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWogLws/file8a582415a0a7.rds")lapply(X = S, FUN = FUN, ...)26:
withVisible(eval(expr, envir))An irrecoverable exception occurred. R is aborting now ...
8:
doTryCatch(return(expr), name, parentenv, handler)27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
{ 9: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (on_message$capture) {
watcher$push(cnd)10: }tryCatchList(expr, classes, parentenv, handlers) if (on_message$silence) {
invokeRestart("muffleMessage") }11: }, warning = function (cnd) tryCatch(expr, error = function(e) {{ call <- conditionCall(e) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) watcher$capture_plot_and_output() call <- sys.call(-4L) if (on_warning$capture) { dcall <- deparse(call, nlines = 1L) cnd <- sanitize_call(cnd) prefix <- paste("Error in", dcall, ": ") watcher$push(cnd) LONG <- 75L } if (on_warning$silence) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] invokeRestart("muffleWarning") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, error = function (cnd) type = "b"){ if (w > LONG) watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) else prefix <- "Error : "}) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))28: if (!silent && isTRUE(getOption("show.error.messages"))) {eval(call) cat(msg, file = outFile)
.Internal(printDeferredWarnings())29: eval(call) }
invisible(structure(msg, class = "try-error", condition = e))30: })with_handlers({
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))12: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
TRUE}, handlers)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))31:
doWithOneRestart(return(expr), restart)
14: 32: FUN(X[[i]], ...)withOneRestart(expr, restarts[[1L]])
15: 33: lapply(seq_len(cores), inner.do)
withRestartList(expr, restarts[-nr])16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)34:
doWithOneRestart(return(expr), restart)
35: 17: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
doTryCatch(return(expr), name, parentenv, handler)36:
18: withRestartList(expr, restarts)tryCatchOne(expr, names, parentenv, handlers[[1L]])
37: 19: withRestarts(with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
20: watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$print_value(ev$value, ev$visible, envir) mc.preschedule = TRUE), error = function(e) NULL)
}21: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)SweepApply(theta, worker, numProcess)
38:
evaluate::evaluate(...)22:
unlist(SweepApply(theta, worker, numProcess))39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", keep_message = if (is.numeric(options$message)) TRUE else options$message, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", stop_on_error = if (is.numeric(options$error)) options$error else { E = E, showPlot = TRUE) if (options$error && options$include)
0L24: else 2Leval(expr, envir) }, output_handler = knit_handlers(options$render, options))
40: 25: in_dir(input_dir(), expr)eval(expr, envir)
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 26: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withVisible(eval(expr, envir)) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {27: if (options$error && options$include) withCallingHandlers(code, error = function (e) 0Lrlang::entrace(e), message = function (cnd) else 2L{ }, output_handler = knit_handlers(options$render, options))) watcher$capture_plot_and_output() if (on_message$capture) {
watcher$push(cnd) }42: if (on_message$silence) {eng_r(options) invokeRestart("muffleMessage")
}43: block_exec(params)}, warning = function (cnd)
{44: if (getOption("warn") >= 2 || getOption("warn") < 0) {call_block(x)
return()45: }process_group(group) watcher$capture_plot_and_output()
if (on_warning$capture) {46: cnd <- sanitize_call(cnd)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) error = function(e) { } if (progress && is.function(pb$interrupt)) pb$interrupt() if (on_warning$silence) { invokeRestart("muffleWarning") if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e)}, error = function (cnd) }){ watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)47: watcher$push(cnd)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) if (progress && is.function(pb$interrupt)) }) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
28: error <<- format(e)eval(call)
}), list(rlang_trace_top_env = knit_global()))29:
48: eval(call)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { if (progress && is.function(pb$interrupt)) 30: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) with_handlers({ error <<- format(e) for (expr in tle$exprs) { }), list(rlang_trace_top_env = knit_global())), function(loc) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() setwd(wd) watcher$print_value(ev$value, ev$visible, envir) write_utf8(res, output %n% stdout()) } paste0("\nQuitting from ", loc, if (!is.null(error)) TRUE paste0("\n", rule(), error, "\n", rule()))}, handlers)
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)31:
doWithOneRestart(return(expr), restart)49:
process_file(text, output)32:
withOneRestart(expr, restarts[[1L]])50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)33:
withRestartList(expr, restarts[-nr])
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 34: output_dir = getwd(), ...)
doWithOneRestart(return(expr), restart)
52: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])vweave_rmarkdown(...)
36: 53: withRestartList(expr, restarts)engine$weave(file, quiet = quiet, encoding = enc)
37: 54: withRestarts(with_handlers({ for (expr in tle$exprs) {doTryCatch(return(expr), name, parentenv, handler)
ev <- withVisible(eval(expr, envir))55: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir) }
TRUE56: tryCatchList(expr, classes, parentenv, handlers)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: 57: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatch({ stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) engine$weave(file, quiet = quiet, encoding = enc) 0L setwd(startdir) else 2L }, output_handler = knit_handlers(options$render, options)) output <- find_vignette_product(name, by = "weave", engine = engine)
40: if (!have.makefile && vignette_is_tex(output)) {in_dir(input_dir(), expr) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 41: engine = engine)in_input_dir(evaluate(code, envir = env, new_device = FALSE, } keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, outputs <- c(outputs, output) keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function(e) { thisOK <<- FALSE stop_on_error = if (is.numeric(options$error)) options$error else { fails <<- c(fails, file) if (options$error && options$include) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 0L file, conditionMessage(e)))}) else 2L
}, output_handler = knit_handlers(options$render, options)))58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 42: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpWogLws/file8a582415a0a7.rds")eng_r(options)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpWogLws/file8a582415a0a7.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