Last updated on 2026-10-17 08:50:28 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.66 | 225.50 | 229.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.47 | 224.20 | 226.67 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 137.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.18 | 212.69 | 215.87 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 6.00 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 35.00 | 37.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 158.00 | 165.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-10-17 15:05:04.697 R[47492:70487] 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'
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]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) 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)
Traceback:
1:
RowCumsum(valid)13:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
2: 14: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, FUN(X[[i]], ...) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)
15: lapply(seq_len(cores), inner.do) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 16: embedded = embedded, validLib = validLib, noTime = noTime, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) ignoreNan = ignoreNan, backend = backend)
17: 4: doTryCatch(return(expr), name, parentenv, handler)ComputeError(predictions$Observations, predictions$Predictions)
18: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 19: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)tryCatchList(expr, classes, parentenv, handlers)
6: 20: FUN(X[[i]], ...)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
7: 21: SweepApply(theta, worker, numProcess)lapply(X = S, FUN = FUN, ...)
8: 22: doTryCatch(return(expr), name, parentenv, handler)unlist(SweepApply(theta, worker, numProcess))
23:
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 11: E = E, showPlot = TRUE)tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (!is.null(call)) {24: if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)eval(expr, envir) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") LONG <- 75L25: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eval(expr, envir) if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG)
prefix <- paste0(prefix, "\n ") }26: else prefix <- "Error : "withVisible(eval(expr, envir))
msg <- paste0(prefix, conditionMessage(e), "\n")27: .Internal(seterrmessage(msg[1L]))withCallingHandlers(code, error = function (e) if (!silent && isTRUE(getOption("show.error.messages"))) {rlang::entrace(e), message = function (cnd) { cat(msg, file = outFile) watcher$capture_plot_and_output() .Internal(printDeferredWarnings()) if (on_message$capture) { } watcher$push(cnd) invisible(structure(msg, class = "try-error", condition = e))}) }
if (on_message$silence) {12: invokeRestart("muffleMessage") }try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: }, warning = function (cnd) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)){
if (getOption("warn") >= 2 || getOption("warn") < 0) {14: return()FUN(X[[i]], ...)
}15: lapply(seq_len(cores), inner.do) watcher$capture_plot_and_output() if (on_warning$capture) {
cnd <- sanitize_call(cnd) watcher$push(cnd)16: }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
if (on_warning$silence) {17: invokeRestart("muffleWarning") }doTryCatch(return(expr), name, parentenv, handler)}, error = function (cnd)
18: {tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)19: watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)20: })tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
21: 28: SweepApply(theta, worker, numProcess)
eval(call)22: unlist(SweepApply(theta, worker, numProcess))
29: 23: eval(call)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
30: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", with_handlers({ E = E, showPlot = TRUE) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()24: watcher$print_value(ev$value, ev$visible, envir) }eval(expr, envir) TRUE}, handlers)
25: 31: doWithOneRestart(return(expr), restart)eval(expr, envir)
32: withOneRestart(expr, restarts[[1L]])26: withVisible(eval(expr, envir))
33: 27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) withRestartList(expr, restarts[-nr]){ watcher$capture_plot_and_output()
if (on_message$capture) {34: watcher$push(cnd)doWithOneRestart(return(expr), restart) }
if (on_message$silence) {35: invokeRestart("muffleMessage")withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }}, warning = function (cnd)
{36: if (getOption("warn") >= 2 || getOption("warn") < 0) {withRestartList(expr, restarts) return()
}37: watcher$capture_plot_and_output() if (on_warning$capture) {withRestarts(with_handlers({ for (expr in tle$exprs) { cnd <- sanitize_call(cnd) ev <- withVisible(eval(expr, envir)) watcher$push(cnd) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) if (on_warning$silence) { } invokeRestart("muffleWarning") TRUE }}, error = function (cnd) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE){
watcher$capture_plot_and_output()38: evaluate::evaluate(...)
cnd <- sanitize_call(cnd)39: watcher$push(cnd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, switch(on_error, continue = invokeRestart("eval_continue"), keep_message = if (is.numeric(options$message)) TRUE else options$message, stop = invokeRestart("eval_stop"), error = NULL) stop_on_error = if (is.numeric(options$error)) options$error else {})
*** caught segfault ***
if (options$error && options$include)
0Laddress 0x110, cause 'invalid permissions'
28: else 2Leval(call) }, output_handler = knit_handlers(options$render, options))
29: eval(call)
30: 40: with_handlers({in_dir(input_dir(), expr)
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUE stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers) if (options$error && options$include)
0L31: else 2LdoWithOneRestart(return(expr), restart) }, output_handler = knit_handlers(options$render, options)))
32: withOneRestart(expr, restarts[[1L]])42:
eng_r(options)33:
withRestartList(expr, restarts[-nr])
43: 34: block_exec(params)doWithOneRestart(return(expr), restart)
44: call_block(x)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
45:
process_group(group)36:
withRestartList(expr, restarts)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 37: error = function(e) { if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({ pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) ev <- withVisible(eval(expr, envir)) }) watcher$capture_plot_and_output()
47: watcher$print_value(ev$value, ev$visible, envir)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { if (progress && is.function(pb$interrupt)) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 39: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))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) 0L48: else 2Lxfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, output_handler = knit_handlers(options$render, options)) error = function(e) {
if (progress && is.function(pb$interrupt)) 40: pb$interrupt()in_dir(input_dir(), expr) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)41: }), list(rlang_trace_top_env = knit_global())), function(loc) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
Traceback:
keep_message = if (is.numeric(options$message)) TRUE else options$message, 1: RowCumsum(valid) setwd(wd) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
write_utf8(res, output %n% stdout()) 0L 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, else 2L validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) paste0("\nQuitting from ", loc, if (!is.null(error))
}, output_handler = knit_handlers(options$render, options))) paste0("\n", rule(), error, "\n", rule())) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) tau = tau, theta = th, exclusionRadius = exclusionRadius, 42:
embedded = embedded, validLib = validLib, noTime = noTime, 49: ignoreNan = ignoreNan, backend = backend)eng_r(options)process_file(text, output)
43:
block_exec(params)50:
4: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)44: ComputeError(predictions$Observations, predictions$Predictions)
call_block(x)
51: 45: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), process_group(group) output_dir = getwd(), ...)
5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 52: 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), vweave_rmarkdown(...) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 53: error = function(e) {engine$weave(file, quiet = quiet, encoding = enc) ignoreNan = ignoreNan, backend = backend)$predictions) if (progress && is.function(pb$interrupt))
pb$interrupt()
54: if (is_R_CMD_build() || is_R_CMD_check()) doTryCatch(return(expr), name, parentenv, handler) 6: error <<- format(e)
})55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])47: FUN(X[[i]], ...)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {56: if (progress && is.function(pb$interrupt)) 7: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)
pb$interrupt() 8:
doTryCatch(return(expr), name, parentenv, handler)57: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch({
engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e) 9: setwd(startdir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }), list(rlang_trace_top_env = knit_global())) output <- find_vignette_product(name, by = "weave", engine = engine)
48: if (!have.makefile && vignette_is_tex(output)) {10: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), texi2pdf(file = output, clean = FALSE, quiet = quiet) error = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt)) output <- find_vignette_product(name, by = "texi2pdf", pb$interrupt() engine = engine)
}11: outputs <- c(outputs, output) if (is_R_CMD_build() || is_R_CMD_check()) tryCatch(expr, error = function(e) {}, error = function(e) { call <- conditionCall(e) error <<- format(e) thisOK <<- FALSE }), list(rlang_trace_top_env = knit_global())), function(loc) { if (!is.null(call)) { fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", setwd(wd) if (identical(call[[1L]], quote(doTryCatch))) file, conditionMessage(e)))}) write_utf8(res, output %n% stdout())
call <- sys.call(-4L) paste0("\nQuitting from ", loc, if (!is.null(error)) dcall <- deparse(call, nlines = 1L)58: paste0("\n", rule(), error, "\n", rule())) prefix <- paste("Error in", dcall, ": ")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", LONG <- 75L}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpnbphwj/file84b14e8face8.rds") sm <- strsplit(conditionMessage(e), "\n")[[1L]]
49: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
process_file(text, output) if (is.na(w)) An irrecoverable exception occurred. R is aborting now ...
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) 50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) prefix <- paste0(prefix, "\n ")
}51: else prefix <- "Error : "rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) output_dir = getwd(), ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)52: .Internal(printDeferredWarnings())vweave_rmarkdown(...) }
invisible(structure(msg, class = "try-error", condition = e))53: })engine$weave(file, quiet = quiet, encoding = enc)
12: 54: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)doTryCatch(return(expr), name, parentenv, handler)
55: 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
56: 14: FUN(X[[i]], ...)tryCatchList(expr, classes, parentenv, handlers)
15: lapply(seq_len(cores), inner.do)57:
tryCatch({16: engine$weave(file, quiet = quiet, encoding = enc)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)17: if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", doTryCatch(return(expr), name, parentenv, handler) engine = engine)
} outputs <- c(outputs, output)18: }, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]])
thisOK <<- FALSE19: fails <<- c(fails, file)tryCatchList(expr, classes, parentenv, handlers) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))
})20:
58: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", mc.preschedule = TRUE), error = function(e) NULL)
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpnbphwj/file84b14e8face8.rds")21:
An irrecoverable exception occurred. R is aborting now ...
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: 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$include) 0L else 2L
Traceback:
}, output_handler = knit_handlers(options$render, options))) 1:
RowCumsum(valid)42:
2: eng_r(options)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 43: tieBreak = FALSE, verbose = verbose)block_exec(params)
3: 44: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, call_block(x) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 45: ignoreNan = ignoreNan, backend = backend)process_group(group)
4: 46: ComputeError(predictions$Observations, predictions$Predictions)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { 5: if (progress && is.function(pb$interrupt)) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, pb$interrupt() knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (is_R_CMD_build() || is_R_CMD_check()) embedded = embedded, validLib = validLib, noTime = noTime, error <<- format(e) ignoreNan = ignoreNan, backend = backend)$predictions) })
47: 6: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {FUN(X[[i]], ...) if (progress && is.function(pb$interrupt))
pb$interrupt() 7: if (is_R_CMD_build() || is_R_CMD_check()) lapply(X = S, FUN = FUN, ...) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))
8: 48: doTryCatch(return(expr), name, parentenv, handler)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) { 9: if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) tryCatchOne(expr, names, parentenv, handlers[[1L]]) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)10: tryCatchList(expr, classes, parentenv, handlers) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 11: paste0("\n", rule(), error, "\n", rule()))tryCatch(expr, error = function(e) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) call <- conditionCall(e) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 49: call <- sys.call(-4L)process_file(text, output) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")50: LONG <- 75Lknitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")51: if (is.na(w)) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], output_dir = getwd(), ...) type = "b")
if (w > LONG) 52: prefix <- paste0(prefix, "\n ")vweave_rmarkdown(...) }
else prefix <- "Error : "53: msg <- paste0(prefix, conditionMessage(e), "\n")engine$weave(file, quiet = quiet, encoding = enc) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {54: cat(msg, file = outFile)doTryCatch(return(expr), name, parentenv, handler) .Internal(printDeferredWarnings())
55: } invisible(structure(msg, class = "try-error", condition = e))tryCatchOne(expr, names, parentenv, handlers[[1L]])})
56: tryCatchList(expr, classes, parentenv, handlers)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)57:
tryCatch({13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: engine$weave(file, quiet = quiet, encoding = enc)FUN(X[[i]], ...) setwd(startdir)
15: output <- find_vignette_product(name, by = "weave", engine = engine)lapply(seq_len(cores), inner.do)
if (!have.makefile && vignette_is_tex(output)) {16: texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) } outputs <- c(outputs, output)
}, error = function(e) {17: doTryCatch(return(expr), name, parentenv, handler) thisOK <<- FALSE
fails <<- c(fails, file)18: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tryCatchOne(expr, names, parentenv, handlers[[1L]]) file, conditionMessage(e)))})
19:
tryCatchList(expr, classes, parentenv, handlers)58:
20: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", tryCatch(parallel::mclapply(values, worker, mc.cores = cores, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmpnbphwj/file84b14e8face8.rds") mc.preschedule = TRUE), error = function(e) NULL)
21: An irrecoverable exception occurred. R is aborting now ...
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: 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()) 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/Rtmpnbphwj/file84b14e8face8.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