Last updated on 2026-10-06 02:53:04 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.06 | 225.28 | 228.34 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.45 | 217.88 | 220.33 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.52 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.10 | 210.00 | 214.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 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 | 5.00 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 9.00 | 161.00 | 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
2026-10-06 12:45:59.028 R[45051:67278] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
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")
Traceback:
if (w > LONG) 1: prefix <- paste0(prefix, "\n ") }RowCumsum(valid) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n") 2: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, cat(msg, file = outFile) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, .Internal(printDeferredWarnings()) tieBreak = FALSE, verbose = verbose) }
invisible(structure(msg, class = "try-error", condition = e)) 3: })SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 12: embedded = embedded, validLib = validLib, noTime = noTime, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) ignoreNan = ignoreNan, backend = backend)
13: 4: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
ComputeError(predictions$Observations, predictions$Predictions)14:
5: FUN(X[[i]], ...)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 15: lapply(seq_len(cores), inner.do) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
16: 6: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)FUN(X[[i]], ...)
17: doTryCatch(return(expr), name, parentenv, handler) 7:
lapply(X = S, FUN = FUN, ...)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8:
doTryCatch(return(expr), name, parentenv, handler)19:
tryCatchList(expr, classes, parentenv, handlers)
9: 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
Traceback:
10: 1: tryCatchList(expr, classes, parentenv, handlers)
RowCumsum(valid)
21: 11: SweepApply(theta, worker, numProcess)tryCatch(expr, error = function(e) {
call <- conditionCall(e)22: 2: if (!is.null(call)) {unlist(SweepApply(theta, worker, numProcess)) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)23: dcall <- deparse(call, nlines = 1L)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", prefix <- paste("Error in", dcall, ": ") E = E, showPlot = TRUE) LONG <- 75L
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, sm <- strsplit(conditionMessage(e), "\n")[[1L]]24: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") tieBreak = FALSE, verbose = verbose) if (is.na(w)) eval(expr, envir) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG) 25: 3: prefix <- paste0(prefix, "\n ")SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, eval(expr, envir) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, } ignoreNan = ignoreNan, backend = backend)26: else prefix <- "Error : "withVisible(eval(expr, envir))
msg <- paste0(prefix, conditionMessage(e), "\n") 4:
.Internal(seterrmessage(msg[1L]))ComputeError(predictions$Observations, predictions$Predictions)27: if (!silent && isTRUE(getOption("show.error.messages"))) {withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) cat(msg, file = outFile){ .Internal(printDeferredWarnings()) watcher$capture_plot_and_output() if (on_message$capture) { 5: watcher$push(cnd) } }SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, invisible(structure(msg, class = "try-error", condition = e)) if (on_message$silence) { knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, }) embedded = embedded, validLib = validLib, noTime = noTime,
invokeRestart("muffleMessage")12: } ignoreNan = ignoreNan, backend = backend)$predictions)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)}, warning = function (cnd)
{13: if (getOption("warn") >= 2 || getOption("warn") < 0) { 6: return()FUN(X[[i]], ...) }
watcher$capture_plot_and_output() 7: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))lapply(X = S, FUN = FUN, ...) if (on_warning$capture) {
cnd <- sanitize_call(cnd) 8: 14: watcher$push(cnd)FUN(X[[i]], ...)doTryCatch(return(expr), name, parentenv, handler)
}
15: if (on_warning$silence) {lapply(seq_len(cores), inner.do) invokeRestart("muffleWarning")
9: 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) }parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)}, error = function (cnd)
17: 10: {tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
watcher$capture_plot_and_output()11: 18: cnd <- sanitize_call(cnd)tryCatch(expr, error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$push(cnd) call <- conditionCall(e)
switch(on_error, continue = invokeRestart("eval_continue"), if (!is.null(call)) {19: stop = invokeRestart("eval_stop"), error = NULL)tryCatchList(expr, classes, parentenv, handlers) if (identical(call[[1L]], quote(doTryCatch))) })
call <- sys.call(-4L)20: 28: dcall <- deparse(call, nlines = 1L)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, eval(call) prefix <- paste("Error in", dcall, ": ") mc.preschedule = TRUE), error = function(e) NULL) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]29:
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eval(call)21: if (is.na(w))
SweepApply(theta, worker, numProcess) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 30:
type = "b")22: if (w > LONG) unlist(SweepApply(theta, worker, numProcess)) prefix <- paste0(prefix, "\n ")with_handlers({
}23: for (expr in tle$exprs) { else prefix <- "Error : " ev <- withVisible(eval(expr, envir))PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output() msg <- paste0(prefix, conditionMessage(e), "\n") target = "Thrips_imaginis", lib = "1 73", pred = "1 73", watcher$print_value(ev$value, ev$visible, envir) E = E, showPlot = TRUE) } .Internal(seterrmessage(msg[1L])) TRUE if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings())}, handlers) }
invisible(structure(msg, class = "try-error", condition = e))31: 24: })doWithOneRestart(return(expr), restart)eval(expr, envir)
32: 25: 12: withOneRestart(expr, restarts[[1L]])eval(expr, envir)
33: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
withRestartList(expr, restarts[-nr])26:
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))withVisible(eval(expr, envir))34:
27: doWithOneRestart(return(expr), restart)14: withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) FUN(X[[i]], ...)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]){
36: watcher$capture_plot_and_output()withRestartList(expr, restarts)15: if (on_message$capture) {lapply(seq_len(cores), inner.do)
watcher$push(cnd)
}16: if (on_message$silence) {37: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
withRestarts(with_handlers({ invokeRestart("muffleMessage") for (expr in tle$exprs) {17: }doTryCatch(return(expr), name, parentenv, handler) ev <- withVisible(eval(expr, envir))
}, warning = function (cnd) watcher$capture_plot_and_output()18: { watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (getOption("warn") >= 2 || getOption("warn") < 0) {
19: }tryCatchList(expr, classes, parentenv, handlers) return()
} TRUE watcher$capture_plot_and_output() if (on_warning$capture) {20: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) cnd <- sanitize_call(cnd)
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$push(cnd)38: mc.preschedule = TRUE), error = function(e) NULL) }evaluate::evaluate(...) if (on_warning$silence) {
invokeRestart("muffleWarning")
}21: }, error = function (cnd) 39: {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, SweepApply(theta, worker, numProcess) watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message,
cnd <- sanitize_call(cnd)22: watcher$push(cnd) stop_on_error = if (is.numeric(options$error)) options$error else {unlist(SweepApply(theta, worker, numProcess)) if (options$error && options$include) 0L switch(on_error, continue = invokeRestart("eval_continue"), else 2L
}, output_handler = knit_handlers(options$render, options)) stop = invokeRestart("eval_stop"), error = NULL)
23: })PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 40:
in_dir(input_dir(), expr)28:
41: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", eval(call)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
29: E = E, showPlot = TRUE)eval(call) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
30: keep_message = if (is.numeric(options$message)) TRUE else options$message, with_handlers({24: eval(expr, envir)
for (expr in tle$exprs) { stop_on_error = if (is.numeric(options$error)) options$error else {25: ev <- withVisible(eval(expr, envir))eval(expr, envir) watcher$capture_plot_and_output() if (options$error && options$include)
watcher$print_value(ev$value, ev$visible, envir)26: } 0LwithVisible(eval(expr, envir)) TRUE
}, handlers) else 2L
}, output_handler = knit_handlers(options$render, options)))31: 27:
doWithOneRestart(return(expr), restart)withCallingHandlers(code, error = function (e)
42: 32: eng_r(options)rlang::entrace(e), message = function (cnd) withOneRestart(expr, restarts[[1L]])
{43:
block_exec(params) watcher$capture_plot_and_output()
33: if (on_message$capture) {withRestartList(expr, restarts[-nr])44:
call_block(x)34:
doWithOneRestart(return(expr), restart)
45: 35: process_group(group) watcher$push(cnd)
}withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_message$silence) { invokeRestart("muffleMessage")
46: }36: withRestartList(expr, restarts)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
}, warning = function (cnd) error = function(e) {37: if (progress && is.function(pb$interrupt)) { pb$interrupt() if (getOption("warn") >= 2 || getOption("warn") < 0) {withRestarts(with_handlers({ for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) return() error <<- format(e) } }) watcher$capture_plot_and_output() watcher$capture_plot_and_output()
if (on_warning$capture) {47: cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir) }with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { TRUE if (on_warning$silence) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) invokeRestart("muffleWarning")
} if (progress && is.function(pb$interrupt)) }, error = function (cnd) pb$interrupt(){38: if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) cnd <- sanitize_call(cnd) watcher$push(cnd) }), list(rlang_trace_top_env = knit_global()))evaluate::evaluate(...) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)48: 39: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt))
pb$interrupt()28: keep_message = if (is.numeric(options$message)) TRUE else options$message, eval(call) stop_on_error = if (is.numeric(options$error)) options$error else { if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)29: if (options$error && options$include) }), list(rlang_trace_top_env = knit_global())), function(loc) { 0Leval(call) setwd(wd) else 2L
write_utf8(res, output %n% stdout()) }, output_handler = knit_handlers(options$render, options))30: paste0("\nQuitting from ", loc, if (!is.null(error)) with_handlers({
for (expr in tle$exprs) {40: ev <- withVisible(eval(expr, envir)) paste0("\n", rule(), error, "\n", rule()))in_dir(input_dir(), expr) watcher$capture_plot_and_output()
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$print_value(ev$value, ev$visible, envir)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 49: }process_file(text, output) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, TRUE
keep_message = if (is.numeric(options$message)) TRUE else options$message, 50: }, handlers) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)31:
0LdoWithOneRestart(return(expr), restart)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 32: output_dir = getwd(), ...) else 2LwithOneRestart(expr, restarts[[1L]]) }, output_handler = knit_handlers(options$render, options)))
33:
52: 42: withRestartList(expr, restarts[-nr])eng_r(options)vweave_rmarkdown(...)
43: 34: 53: block_exec(params)doWithOneRestart(return(expr), restart)engine$weave(file, quiet = quiet, encoding = enc)
44:
call_block(x)35:
54: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])45: doTryCatch(return(expr), name, parentenv, handler)process_group(group)
36:
55: withRestartList(expr, restarts)
tryCatchOne(expr, names, parentenv, handlers[[1L]])46: 37:
Traceback:
withRestarts(with_handlers({withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
56: 1: for (expr in tle$exprs) { error = function(e) {RowCumsum(valid) if (progress && is.function(pb$interrupt)) ev <- withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers)
watcher$capture_plot_and_output() pb$interrupt() 2: 57: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, if (is_R_CMD_build() || is_R_CMD_check()) watcher$print_value(ev$value, ev$visible, envir)tryCatch({ error <<- format(e) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }) } engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir) tieBreak = FALSE, verbose = verbose)47: output <- find_vignette_product(name, by = "weave", engine = engine)
TRUEwith_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (!have.makefile && vignette_is_tex(output)) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
3: 38: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, evaluate::evaluate(...) texi2pdf(file = output, clean = FALSE, quiet = quiet) error = function(e) {
output <- find_vignette_product(name, by = "texi2pdf", tau = tau, theta = th, exclusionRadius = exclusionRadius, if (progress && is.function(pb$interrupt)) engine = engine) pb$interrupt() }39: outputs <- c(outputs, output)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) { error <<- format(e) keep_message = if (is.numeric(options$message)) TRUE else options$message, }), list(rlang_trace_top_env = knit_global())) embedded = embedded, validLib = validLib, noTime = noTime, thisOK <<- FALSE
ignoreNan = ignoreNan, backend = backend)48: fails <<- c(fails, file) stop_on_error = if (is.numeric(options$error)) options$error else {
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 4: if (options$error && options$include) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", ComputeError(predictions$Observations, predictions$Predictions) file, conditionMessage(e)))
0L}) 5: else 2L error = function(e) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, if (progress && is.function(pb$interrupt)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
}, output_handler = knit_handlers(options$render, options)) embedded = embedded, validLib = validLib, noTime = noTime, pb$interrupt()
ignoreNan = ignoreNan, backend = backend)$predictions)40: 58: if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 6: in_dir(input_dir(), expr) }), list(rlang_trace_top_env = knit_global())), function(loc) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpxActPE/file840f5fc8ea75.rds")
FUN(X[[i]], ...)An irrecoverable exception occurred. R is aborting now ...
41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 7: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(X = S, FUN = FUN, ...)
8: keep_message = if (is.numeric(options$message)) TRUE else options$message, doTryCatch(return(expr), name, parentenv, handler)
stop_on_error = if (is.numeric(options$error)) options$error else { 9: setwd(wd) if (options$error && options$include) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L write_utf8(res, output %n% stdout())
else 2L paste0("\nQuitting from ", loc, if (!is.null(error)) }, output_handler = knit_handlers(options$render, options))) paste0("\n", rule(), error, "\n", rule()))10: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatchList(expr, classes, parentenv, handlers)
49:
11: process_file(text, output)tryCatch(expr, error = function(e) {42:
call <- conditionCall(e)eng_r(options)50: if (!is.null(call)) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
if (identical(call[[1L]], quote(doTryCatch))) 43:
call <- sys.call(-4L)block_exec(params) dcall <- deparse(call, nlines = 1L)51: prefix <- paste("Error in", dcall, ": ")
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), LONG <- 75L output_dir = getwd(), ...)44: sm <- strsplit(conditionMessage(e), "\n")[[1L]]
call_block(x) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 52: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 45: vweave_rmarkdown(...)process_group(group) type = "b")
if (w > LONG) 46: 53: prefix <- paste0(prefix, "\n ")engine$weave(file, quiet = quiet, encoding = enc)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }
error = function(e) { else prefix <- "Error : " if (progress && is.function(pb$interrupt)) msg <- paste0(prefix, conditionMessage(e), "\n")54: .Internal(seterrmessage(msg[1L])) pb$interrupt() if (!silent && isTRUE(getOption("show.error.messages"))) {doTryCatch(return(expr), name, parentenv, handler) cat(msg, file = outFile) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)55: .Internal(printDeferredWarnings()) }) }tryCatchOne(expr, names, parentenv, handlers[[1L]]) invisible(structure(msg, class = "try-error", condition = e))
})56:
47: 12: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchList(expr, classes, parentenv, handlers)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
error = function(e) {
57: if (progress && is.function(pb$interrupt)) 13: pb$interrupt()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (is_R_CMD_build() || is_R_CMD_check()) tryCatch({
engine$weave(file, quiet = quiet, encoding = enc) error <<- format(e) setwd(startdir)14: }), list(rlang_trace_top_env = knit_global()))FUN(X[[i]], ...)
output <- find_vignette_product(name, by = "weave", engine = engine)15:
lapply(seq_len(cores), inner.do) if (!have.makefile && vignette_is_tex(output)) {
48: texi2pdf(file = output, clean = FALSE, quiet = quiet)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 16: output <- find_vignette_product(name, by = "texi2pdf", error = function(e) { engine = engine) } if (progress && is.function(pb$interrupt)) outputs <- c(outputs, output)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) pb$interrupt()
17: if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) {doTryCatch(return(expr), name, parentenv, handler) error <<- format(e)
thisOK <<- FALSE18: }), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e))) setwd(wd)})19: tryCatchList(expr, classes, parentenv, handlers)
write_utf8(res, output %n% stdout())
58: paste0("\nQuitting from ", loc, if (!is.null(error)) tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpxActPE/file840f5fc8ea75.rds") paste0("\n", rule(), error, "\n", rule()))
An irrecoverable exception occurred. R is aborting now ...
20: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)49:
process_file(text, output)21:
50: SweepApply(theta, worker, numProcess)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
22: 51: unlist(SweepApply(theta, worker, numProcess))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)23:
52: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", vweave_rmarkdown(...)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 53: E = E, showPlot = TRUE)engine$weave(file, quiet = quiet, encoding = enc)
24: 54: eval(expr, envir)doTryCatch(return(expr), name, parentenv, handler)
25: 55: eval(expr, envir)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])withVisible(eval(expr, envir))
56: 27: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 57: {tryCatch({ watcher$capture_plot_and_output() engine$weave(file, quiet = quiet, encoding = enc) if (on_message$capture) { setwd(startdir) watcher$push(cnd) output <- find_vignette_product(name, by = "weave", engine = engine) } if (!have.makefile && vignette_is_tex(output)) { if (on_message$silence) { texi2pdf(file = output, clean = FALSE, quiet = quiet) invokeRestart("muffleMessage") output <- find_vignette_product(name, by = "texi2pdf", } engine = engine)}, warning = function (cnd) }{ outputs <- c(outputs, output) if (getOption("warn") >= 2 || getOption("warn") < 0) {}, error = function(e) { return() thisOK <<- FALSE } watcher$capture_plot_and_output() if (on_warning$capture) { fails <<- c(fails, file) cnd <- sanitize_call(cnd) watcher$push(cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", } file, conditionMessage(e))) if (on_warning$silence) {}) invokeRestart("muffleWarning") }
}, error = function (cnd) 58: {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", watcher$capture_plot_and_output() skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpxActPE/file840f5fc8ea75.rds") cnd <- sanitize_call(cnd)
An irrecoverable exception occurred. R is aborting now ...
watcher$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/RtmpxActPE/file840f5fc8ea75.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