Last updated on 2026-11-05 05:55:59 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.59 | 220.83 | 224.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.36 | 244.70 | 247.06 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.37 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | OK | ||||
| r-release-linux-x86_64 | 2.0.2 | 2.79 | 206.57 | 209.36 | 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 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 38.00 | 40.00 | 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 | 155.00 | 161.00 | 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
2026-11-05 14:07:00.916 R[43435:68352] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
Traceback:
1: 3: RowCumsum(valid)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 2: embedded = embedded, validLib = validLib, noTime = noTime, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose) 4:
ComputeError(predictions$Observations, predictions$Predictions) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 5: tau = tau, theta = th, exclusionRadius = exclusionRadius, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, embedded = embedded, validLib = validLib, noTime = noTime, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, ignoreNan = ignoreNan, backend = backend)
embedded = embedded, validLib = validLib, noTime = noTime, 4: ignoreNan = ignoreNan, backend = backend)$predictions)ComputeError(predictions$Observations, predictions$Predictions)
6: 5: FUN(X[[i]], ...)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
7: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, lapply(X = S, FUN = FUN, ...) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
8: 6: doTryCatch(return(expr), name, parentenv, handler)FUN(X[[i]], ...)
9: 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])lapply(X = S, FUN = FUN, ...)
10:
tryCatchList(expr, classes, parentenv, handlers) 8:
doTryCatch(return(expr), name, parentenv, handler)11:
tryCatch(expr, error = function(e) { 9: call <- conditionCall(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 10: call <- sys.call(-4L)tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")11: LONG <- 75LtryCatch(expr, error = function(e) { call <- conditionCall(e) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (!is.null(call)) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (identical(call[[1L]], quote(doTryCatch))) if (is.na(w)) call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") type = "b") LONG <- 75L if (w > LONG) sm <- strsplit(conditionMessage(e), "\n")[[1L]] 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], msg <- paste0(prefix, conditionMessage(e), "\n") type = "b") .Internal(seterrmessage(msg[1L])) if (w > LONG) if (!silent && isTRUE(getOption("show.error.messages"))) { prefix <- paste0(prefix, "\n ") cat(msg, file = outFile) } .Internal(printDeferredWarnings()) else prefix <- "Error : " } 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)
12: .Internal(printDeferredWarnings())try(lapply(X = S, FUN = FUN, ...), silent = TRUE) } invisible(structure(msg, class = "try-error", condition = e))
})13:
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: 14: FUN(X[[i]], ...)FUN(X[[i]], ...)
15: 15: lapply(seq_len(cores), inner.do)lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)17: doTryCatch(return(expr), name, parentenv, handler)
18: 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
19: 18: tryCatchList(expr, classes, parentenv, handlers)tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 20: tryCatchList(expr, classes, parentenv, handlers)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 20: mc.preschedule = TRUE), error = function(e) NULL)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
21: 21: SweepApply(theta, worker, numProcess)SweepApply(theta, worker, numProcess)
22:
22: unlist(SweepApply(theta, worker, numProcess))unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 23: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", E = E, showPlot = TRUE) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)24:
eval(expr, envir)
25: 24: eval(expr, envir)eval(expr, envir)
26: 25: withVisible(eval(expr, envir))eval(expr, envir)
27:
26: withCallingHandlers(code, error = function (e) withVisible(eval(expr, envir))rlang::entrace(e), message = function (cnd)
{ watcher$capture_plot_and_output()27: if (on_message$capture) {withCallingHandlers(code, error = function (e) watcher$push(cnd)rlang::entrace(e), message = function (cnd) }{ if (on_message$silence) { invokeRestart("muffleMessage") watcher$capture_plot_and_output() } if (on_message$capture) {}, warning = function (cnd) watcher$push(cnd){ } if (on_message$silence) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() invokeRestart("muffleMessage") } } watcher$capture_plot_and_output()}, warning = function (cnd) if (on_warning$capture) {{ cnd <- sanitize_call(cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd) return() } if (on_warning$silence) { } invokeRestart("muffleWarning") watcher$capture_plot_and_output() } if (on_warning$capture) {}, error = function (cnd) { cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd) if (on_warning$silence) { watcher$push(cnd) invokeRestart("muffleWarning") switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL)}, error = function (cnd) }){
watcher$capture_plot_and_output()28: cnd <- sanitize_call(cnd)eval(call) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 29: eval(call) stop = invokeRestart("eval_stop"), error = NULL)
})
30: with_handlers({28: for (expr in tle$exprs) {eval(call) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)29: }eval(call) TRUE
}, handlers)30:
with_handlers({31: for (expr in tle$exprs) {doWithOneRestart(return(expr), restart) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
watcher$print_value(ev$value, ev$visible, envir)35: } TRUE}, handlers)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36:
withRestartList(expr, restarts)31:
doWithOneRestart(return(expr), restart)
37: 32: withRestarts(with_handlers({withOneRestart(expr, restarts[[1L]]) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))33: watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr]) watcher$print_value(ev$value, ev$visible, envir)
34: } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, doWithOneRestart(return(expr), restart) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 35: 0L else 2L }, output_handler = knit_handlers(options$render, options))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
40:
in_dir(input_dir(), expr)36:
withRestartList(expr, restarts)41:
37: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withRestarts(with_handlers({ for (expr in tle$exprs) { keep_message = if (is.numeric(options$message)) TRUE else options$message, ev <- withVisible(eval(expr, envir)) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L watcher$capture_plot_and_output() else 2L watcher$print_value(ev$value, ev$visible, envir) }, output_handler = knit_handlers(options$render, options))) } TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
42: 38: eng_r(options)evaluate::evaluate(...)
43: 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, block_exec(params) keep_message = if (is.numeric(options$message)) TRUE else options$message,
44: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0Lcall_block(x) else 2L
45: }, output_handler = knit_handlers(options$render, options))
process_group(group)40:
in_dir(input_dir(), expr)
46: 41: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), in_input_dir(evaluate(code, envir = env, new_device = FALSE, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt)) keep_message = if (is.numeric(options$message)) TRUE else options$message, pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check()) if (options$error && options$include) error <<- format(e) 0L else 2L }, output_handler = knit_handlers(options$render, options))) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 42: pb$interrupt()eng_r(options)
if (is_R_CMD_build() || is_R_CMD_check()) 43: error <<- format(e)block_exec(params) }), list(rlang_trace_top_env = knit_global()))
44: call_block(x)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: error = function(e) {process_group(group) if (progress && is.function(pb$interrupt))
pb$interrupt()46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(e) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt()
Traceback:
setwd(wd) if (is_R_CMD_build() || is_R_CMD_check()) 1: write_utf8(res, output %n% stdout()) error <<- format(e) paste0("\nQuitting from ", loc, if (!is.null(error)) RowCumsum(valid) })
paste0("\n", rule(), error, "\n", rule())) 2: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 47: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
3: error = function(e) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (progress && is.function(pb$interrupt)) tau = tau, theta = th, exclusionRadius = exclusionRadius, pb$interrupt()
49: embedded = embedded, validLib = validLib, noTime = noTime, process_file(text, output) if (is_R_CMD_build() || is_R_CMD_check()) ignoreNan = ignoreNan, backend = backend) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())) 4:
48: ComputeError(predictions$Observations, predictions$Predictions)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
50: 5: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, error = function(e) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (progress && is.function(pb$interrupt))
pb$interrupt()51: if (is_R_CMD_build() || is_R_CMD_check()) rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) error <<- format(e) embedded = embedded, validLib = validLib, noTime = noTime, }), list(rlang_trace_top_env = knit_global())), function(loc) { ignoreNan = ignoreNan, backend = backend)$predictions) setwd(wd)
write_utf8(res, output %n% stdout()) 6: 52: FUN(X[[i]], ...) paste0("\nQuitting from ", loc, if (!is.null(error)) vweave_rmarkdown(...) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
7: 49: lapply(X = S, FUN = FUN, ...)53:
process_file(text, output)engine$weave(file, quiet = quiet, encoding = enc) 8:
doTryCatch(return(expr), name, parentenv, handler)54: 50:
doTryCatch(return(expr), name, parentenv, handler)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])10:
tryCatchList(expr, classes, parentenv, handlers)51: 56:
tryCatchList(expr, classes, parentenv, handlers)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
11: output_dir = getwd(), ...)57: tryCatch(expr, error = function(e) {
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)52: call <- conditionCall(e) setwd(startdir)vweave_rmarkdown(...) output <- find_vignette_product(name, by = "weave", engine = engine) if (!is.null(call)) {
if (!have.makefile && vignette_is_tex(output)) {53: if (identical(call[[1L]], quote(doTryCatch))) texi2pdf(file = output, clean = FALSE, quiet = quiet)engine$weave(file, quiet = quiet, encoding = enc)
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) output <- find_vignette_product(name, by = "texi2pdf", prefix <- paste("Error in", dcall, ": ") LONG <- 75L54: doTryCatch(return(expr), name, parentenv, handler) sm <- strsplit(conditionMessage(e), "\n")[[1L]] engine = engine)
}55: outputs <- c(outputs, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function(e) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
thisOK <<- FALSE if (is.na(w)) fails <<- c(fails, file)56: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") file, conditionMessage(e))) if (w > LONG) 57: tryCatch({ prefix <- paste0(prefix, "\n ")}) }
engine$weave(file, quiet = quiet, encoding = enc) else prefix <- "Error : "58: msg <- paste0(prefix, conditionMessage(e), "\n") setwd(startdir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", .Internal(seterrmessage(msg[1L])) output <- find_vignette_product(name, by = "weave", engine = engine) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdTPn2P/file9a471518f299.rds") if (!have.makefile && vignette_is_tex(output)) { if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)An irrecoverable exception occurred. R is aborting now ...
texi2pdf(file = output, clean = FALSE, quiet = quiet) .Internal(printDeferredWarnings()) output <- find_vignette_product(name, by = "texi2pdf", } engine = engine) invisible(structure(msg, class = "try-error", condition = e)) } outputs <- c(outputs, output)})}, error = function(e) {
12: thisOK <<- FALSEtry(lapply(X = S, FUN = FUN, ...), silent = TRUE) fails <<- c(fails, file)
13: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) file, conditionMessage(e)))})
14: 58: FUN(X[[i]], ...)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdTPn2P/file9a471518f299.rds")15:
An irrecoverable exception occurred. R is aborting now ...
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: 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$push(cnd) }
Traceback:
if (on_message$silence) { 1: RowCumsum(valid) invokeRestart("muffleMessage")
} 2: }, warning = function (cnd) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose){
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, if (getOption("warn") >= 2 || getOption("warn") < 0) { return() ignoreNan = ignoreNan, backend = backend)
} 4: ComputeError(predictions$Observations, predictions$Predictions)
watcher$capture_plot_and_output() 5: if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) }SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (on_warning$silence) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, invokeRestart("muffleWarning") embedded = embedded, validLib = validLib, noTime = noTime, } ignoreNan = ignoreNan, backend = backend)$predictions)}, error = function (cnd) { watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd) 6: watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)FUN(X[[i]], ...)
7: })lapply(X = S, FUN = FUN, ...)
28: 8: eval(call)doTryCatch(return(expr), name, parentenv, handler)
29: 9: eval(call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: 10: with_handlers({ for (expr in tle$exprs) {tryCatchList(expr, classes, parentenv, handlers) ev <- withVisible(eval(expr, envir))
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) watcher$capture_plot_and_output() if (!is.null(call)) { watcher$print_value(ev$value, ev$visible, envir) if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) TRUE dcall <- deparse(call, nlines = 1L)}, handlers) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]31: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doWithOneRestart(return(expr), restart)
if (is.na(w)) 32: withOneRestart(expr, restarts[[1L]]) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) prefix <- paste0(prefix, "\n ")33: }withRestartList(expr, restarts[-nr]) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")34: .Internal(seterrmessage(msg[1L]))doWithOneRestart(return(expr), restart) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)35: .Internal(printDeferredWarnings())withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) } invisible(structure(msg, class = "try-error", condition = e))})
36: withRestartList(expr, restarts)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
37:
withRestarts(with_handlers({13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
for (expr in tle$exprs) {15: 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(...)
lapply(seq_len(cores), inner.do)39:
16: 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, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler) stop_on_error = if (is.numeric(options$error)) options$error else {
18: if (options$error && options$include) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L else 2L
19: }, output_handler = knit_handlers(options$render, options))
tryCatchList(expr, classes, parentenv, handlers)
40: 20: in_dir(input_dir(), expr)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 21: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SweepApply(theta, worker, numProcess) keep_message = if (is.numeric(options$message)) TRUE else options$message,
22: stop_on_error = if (is.numeric(options$error)) options$error else {unlist(SweepApply(theta, worker, numProcess)) if (options$error && options$include)
0L else 2L23: }, output_handler = knit_handlers(options$render, options)))PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 42: E = E, showPlot = TRUE)
eng_r(options)24:
eval(expr, envir)43:
block_exec(params)25:
eval(expr, envir)44:
call_block(x)26: withVisible(eval(expr, envir))
45: process_group(group)27:
withCallingHandlers(code, error = function (e) 46: rlang::entrace(e), message = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {{ if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() pb$interrupt() if (on_message$capture) { if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) } error <<- format(e) if (on_message$silence) { }) invokeRestart("muffleMessage") }
}, warning = function (cnd) 47: {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (getOption("warn") >= 2 || getOption("warn") < 0) { error = function(e) { return() if (progress && is.function(pb$interrupt)) } pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() if (on_warning$capture) { error <<- format(e) cnd <- sanitize_call(cnd) watcher$push(cnd) }), list(rlang_trace_top_env = knit_global())) }
48: if (on_warning$silence) { invokeRestart("muffleWarning")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) {}, error = function (cnd) if (progress && is.function(pb$interrupt)) { pb$interrupt() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) setwd(wd)}) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 28: eval(call) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)29:
49: eval(call)
process_file(text, output)30: with_handlers({
for (expr in tle$exprs) {50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) watcher$print_value(ev$value, ev$visible, envir)
} TRUE52: }, handlers)vweave_rmarkdown(...)
31: doWithOneRestart(return(expr), restart)53:
32: withOneRestart(expr, restarts[[1L]])engine$weave(file, quiet = quiet, encoding = enc)
33:
withRestartList(expr, restarts[-nr])54:
34: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
55: 35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
36:
56: withRestartList(expr, restarts)
37: tryCatchList(expr, classes, parentenv, handlers)
withRestarts(with_handlers({57: for (expr in tle$exprs) {tryCatch({ ev <- withVisible(eval(expr, envir)) engine$weave(file, quiet = quiet, encoding = enc) watcher$capture_plot_and_output() setwd(startdir) watcher$print_value(ev$value, ev$visible, envir) output <- find_vignette_product(name, by = "weave", engine = engine) } if (!have.makefile && vignette_is_tex(output)) { TRUE texi2pdf(file = output, clean = FALSE, quiet = quiet)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)38: } outputs <- c(outputs, output)evaluate::evaluate(...)
}, error = function(e) {39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", keep_message = if (is.numeric(options$message)) TRUE else options$message, file, conditionMessage(e))) stop_on_error = if (is.numeric(options$error)) options$error else {}) if (options$error && options$include)
58: 0Ltools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", else 2L skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpdTPn2P/file9a471518f299.rds") }, output_handler = knit_handlers(options$render, options))
40: An irrecoverable exception occurred. R is aborting now ...
in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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/RtmpdTPn2P/file9a471518f299.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