Last updated on 2026-09-25 00:50:20 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.27 | 226.93 | 230.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.56 | 231.05 | 233.61 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.47 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 141.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.72 | 205.17 | 208.89 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 2.82 | 212.42 | 215.24 | 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 | 130.00 | 136.00 | 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 | 8.00 | 162.00 | 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
2026-09-25 05:35:10.464 R[59162:89980] 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") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: 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()
Traceback:
} 1: watcher$capture_plot_and_output()RowCumsum(valid) if (on_warning$capture) {
cnd <- sanitize_call(cnd) 2: watcher$push(cnd)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, } if (on_warning$silence) { invokeRestart("muffleWarning") } tieBreak = FALSE, verbose = verbose)}, error = function (cnd)
{ 3: watcher$capture_plot_and_output() cnd <- sanitize_call(cnd)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, watcher$push(cnd) tau = tau, theta = th, exclusionRadius = exclusionRadius, switch(on_error, continue = invokeRestart("eval_continue"), embedded = embedded, validLib = validLib, noTime = noTime, stop = invokeRestart("eval_stop"), error = NULL) ignoreNan = ignoreNan, backend = backend)})
28:
4: eval(call)ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 29: eval(call) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)30:
with_handlers({ 6: for (expr in tle$exprs) {FUN(X[[i]], ...) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() 7: lapply(X = S, FUN = FUN, ...) watcher$print_value(ev$value, ev$visible, envir)
} 8: TRUEdoTryCatch(return(expr), name, parentenv, handler)}, handlers)
9: 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
doWithOneRestart(return(expr), restart)10:
tryCatchList(expr, classes, parentenv, handlers)32:
withOneRestart(expr, restarts[[1L]])11:
tryCatch(expr, error = function(e) { call <- conditionCall(e)33: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) withRestartList(expr, restarts[-nr]) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)34: prefix <- paste("Error in", dcall, ": ")doWithOneRestart(return(expr), restart) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]35: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 36: type = "b")withRestartList(expr, restarts) if (w > LONG)
prefix <- paste0(prefix, "\n ")37: }withRestarts(with_handlers({
Traceback:
1: for (expr in tle$exprs) { else prefix <- "Error : "RowCumsum(valid) msg <- paste0(prefix, conditionMessage(e), "\n") ev <- withVisible(eval(expr, envir))
Traceback:
watcher$capture_plot_and_output()
.Internal(seterrmessage(msg[1L])) watcher$print_value(ev$value, ev$visible, envir) 1: } TRUE if (!silent && isTRUE(getOption("show.error.messages"))) { 2: cat(msg, file = outFile)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, RowCumsum(valid) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: 38: evaluate::evaluate(...) 2:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tau = tau, theta = th, exclusionRadius = exclusionRadius, 39: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, embedded = embedded, validLib = validLib, noTime = noTime, tieBreak = FALSE, verbose = verbose) ignoreNan = ignoreNan, backend = backend) keep_message = if (is.numeric(options$message)) TRUE else options$message,
4: stop_on_error = if (is.numeric(options$error)) options$error else { .Internal(printDeferredWarnings()) 3: ComputeError(predictions$Observations, predictions$Predictions) if (options$error && options$include) } 0L invisible(structure(msg, class = "try-error", condition = e)) else 2L
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, }) 5: tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, ignoreNan = ignoreNan, backend = backend) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
}, output_handler = knit_handlers(options$render, options)) 4:
12: embedded = embedded, validLib = validLib, noTime = noTime, 40: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) ignoreNan = ignoreNan, backend = backend)$predictions)in_dir(input_dir(), expr)ComputeError(predictions$Observations, predictions$Predictions)
41: 6: in_input_dir(evaluate(code, envir = env, new_device = FALSE, FUN(X[[i]], ...) 5: 13: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 7: lapply(X = S, FUN = FUN, ...)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 8:
doTryCatch(return(expr), name, parentenv, handler) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 9: 0L14: else 2L embedded = embedded, validLib = validLib, noTime = noTime, FUN(X[[i]], ...) }, output_handler = knit_handlers(options$render, options))) ignoreNan = ignoreNan, backend = backend)$predictions)
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6:
15: 42: FUN(X[[i]], ...)
eng_r(options)
lapply(seq_len(cores), inner.do)
10:
tryCatchList(expr, classes, parentenv, handlers)43:
7: 11: 16: lapply(X = S, FUN = FUN, ...)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)block_exec(params)
17: 8: doTryCatch(return(expr), name, parentenv, handler)tryCatch(expr, error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
44: call <- conditionCall(e)call_block(x)
45: if (!is.null(call)) {18: if (identical(call[[1L]], quote(doTryCatch))) 9: call <- sys.call(-4L)process_group(group)tryCatchOne(expr, names, parentenv, handlers[[1L]]) dcall <- deparse(call, nlines = 1L)
19: 46: tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
20: LONG <- 75LtryCatch(parallel::mclapply(values, worker, mc.cores = cores, 10: mc.preschedule = TRUE), error = function(e) NULL) error = function(e) {tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt))
sm <- strsplit(conditionMessage(e), "\n")[[1L]]21:
SweepApply(theta, worker, numProcess) pb$interrupt()11: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch(expr, error = function(e) { error <<- format(e) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") call <- conditionCall(e) if (!is.null(call)) {
if (is.na(w)) }) if (identical(call[[1L]], quote(doTryCatch)))
22: 47: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- sys.call(-4L) type = "b") if (w > LONG) unlist(SweepApply(theta, worker, numProcess)) prefix <- paste0(prefix, "\n ")with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) {
else prefix <- "Error : "23: msg <- paste0(prefix, conditionMessage(e), "\n") dcall <- deparse(call, nlines = 1L) if (progress && is.function(pb$interrupt)) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", .Internal(seterrmessage(msg[1L])) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", pb$interrupt() if (!silent && isTRUE(getOption("show.error.messages"))) { if (is_R_CMD_build() || is_R_CMD_check()) prefix <- paste("Error in", dcall, ": ") cat(msg, file = outFile) E = E, showPlot = TRUE) error <<- format(e) .Internal(printDeferredWarnings()) } LONG <- 75L
invisible(structure(msg, class = "try-error", condition = e)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] }), list(rlang_trace_top_env = knit_global())) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")24: if (is.na(w))
eval(expr, envir)48: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
}) type = "b")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
25: if (w > LONG) 12: eval(expr, envir) prefix <- paste0(prefix, "\n ")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
error = function(e) {13: else prefix <- "Error : "
if (progress && is.function(pb$interrupt)) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) msg <- paste0(prefix, conditionMessage(e), "\n") pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 26: .Internal(seterrmessage(msg[1L]))withVisible(eval(expr, envir)) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)14: 27: error <<- format(e)withCallingHandlers(code, error = function (e) FUN(X[[i]], ...) .Internal(printDeferredWarnings()) }), list(rlang_trace_top_env = knit_global())), function(loc) {rlang::entrace(e), message = function (cnd)
{ setwd(wd) } write_utf8(res, output %n% stdout()) watcher$capture_plot_and_output()15: if (on_message$capture) { invisible(structure(msg, class = "try-error", condition = e)) paste0("\nQuitting from ", loc, if (!is.null(error)) watcher$push(cnd) paste0("\n", rule(), error, "\n", rule()))lapply(seq_len(cores), inner.do)})}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }
if (on_message$silence) {49: 16: process_file(text, output)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
invokeRestart("muffleMessage")17: 12: 50: doTryCatch(return(expr), name, parentenv, handler)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)13:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) }51:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))19: }, warning = function (cnd) tryCatchList(expr, classes, parentenv, handlers){
if (getOption("warn") >= 2 || getOption("warn") < 0) { return()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
14: }20: watcher$capture_plot_and_output()tryCatch(parallel::mclapply(values, worker, mc.cores = cores, output_dir = getwd(), ...)FUN(X[[i]], ...) if (on_warning$capture) {
cnd <- sanitize_call(cnd)
watcher$push(cnd)15: 52: } mc.preschedule = TRUE), error = function(e) NULL)vweave_rmarkdown(...)lapply(seq_len(cores), inner.do) if (on_warning$silence) {
16: invokeRestart("muffleWarning")parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) }
53: }, error = function (cnd)
engine$weave(file, quiet = quiet, encoding = enc){17: 21: doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()SweepApply(theta, worker, numProcess) cnd <- sanitize_call(cnd)
watcher$push(cnd)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) switch(on_error, continue = invokeRestart("eval_continue"), 54: 22:
doTryCatch(return(expr), name, parentenv, handler)unlist(SweepApply(theta, worker, numProcess)) stop = invokeRestart("eval_stop"), error = NULL)
19: })tryCatchList(expr, classes, parentenv, handlers)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 23: 28: 56: mc.preschedule = TRUE), error = function(e) NULL)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tryCatchList(expr, classes, parentenv, handlers)21: eval(call) E = E, showPlot = TRUE)SweepApply(theta, worker, numProcess)
24:
29:
eval(expr, envir)22: unlist(SweepApply(theta, worker, numProcess))eval(call)
57: 25: tryCatch({
eval(expr, envir) engine$weave(file, quiet = quiet, encoding = enc)
23: 30: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", with_handlers({26: setwd(startdir) for (expr in tle$exprs) { target = "Thrips_imaginis", lib = "1 73", pred = "1 73", output <- find_vignette_product(name, by = "weave", engine = engine) E = E, showPlot = TRUE)withVisible(eval(expr, envir)) if (!have.makefile && vignette_is_tex(output)) {
27: ev <- withVisible(eval(expr, envir))24: eval(expr, envir) texi2pdf(file = output, clean = FALSE, quiet = quiet)
25: output <- find_vignette_product(name, by = "texi2pdf", engine = engine)withCallingHandlers(code, error = function (e) watcher$capture_plot_and_output()rlang::entrace(e), message = function (cnd) { } watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) if (on_message$capture) { outputs <- c(outputs, output) watcher$push(cnd)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)eval(expr, envir) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", } file, conditionMessage(e)))
})26: if (on_message$silence) {
TRUE58: }, handlers)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
withVisible(eval(expr, envir)) invokeRestart("muffleMessage")
31: }}, warning = function (cnd) 27: doWithOneRestart(return(expr), restart){
if (getOption("warn") >= 2 || getOption("warn") < 0) {withCallingHandlers(code, error = function (e) return()32: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1DLhMx/fileabe51e9774bd.rds")withOneRestart(expr, restarts[[1L]])rlang::entrace(e), message = function (cnd)
{33: } watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) {
withRestartList(expr, restarts[-nr])An irrecoverable exception occurred. R is aborting now ...
if (on_message$capture) {
cnd <- sanitize_call(cnd)34: doWithOneRestart(return(expr), restart)
watcher$push(cnd)35: watcher$push(cnd) } if (on_message$silence) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }
invokeRestart("muffleMessage") if (on_warning$silence) { } invokeRestart("muffleWarning")36: }}, warning = function (cnd) }, error = function (cnd) { watcher$capture_plot_and_output()withRestartList(expr, restarts) cnd <- sanitize_call(cnd){
watcher$push(cnd)37: if (getOption("warn") >= 2 || getOption("warn") < 0) { switch(on_error, continue = invokeRestart("eval_continue"), return() stop = invokeRestart("eval_stop"), error = NULL) }})withRestarts(with_handlers({
watcher$capture_plot_and_output()28: for (expr in tle$exprs) { if (on_warning$capture) {eval(call) ev <- withVisible(eval(expr, envir)) cnd <- sanitize_call(cnd) watcher$capture_plot_and_output() watcher$push(cnd) watcher$print_value(ev$value, ev$visible, envir)
}29: } TRUEeval(call)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (on_warning$silence) {
invokeRestart("muffleWarning")38: }30: }, error = function (cnd) evaluate::evaluate(...){with_handlers({ watcher$capture_plot_and_output() for (expr in tle$exprs) { cnd <- sanitize_call(cnd) ev <- withVisible(eval(expr, envir)) watcher$push(cnd) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)39: switch(on_error, continue = invokeRestart("eval_continue"), evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, stop = invokeRestart("eval_stop"), error = NULL) keep_message = if (is.numeric(options$message)) TRUE else options$message, })
stop_on_error = if (is.numeric(options$error)) options$error else {28: } if (options$error && options$include) TRUEeval(call)}, handlers) 0L
31: doWithOneRestart(return(expr), restart)29:
eval(call) else 2L
}, output_handler = knit_handlers(options$render, options))30:
32: 40: withOneRestart(expr, restarts[[1L]])in_dir(input_dir(), expr)
33: with_handlers({
withRestartList(expr, restarts[-nr]) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()34: watcher$print_value(ev$value, ev$visible, envir)doWithOneRestart(return(expr), restart)41:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 35: }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) TRUE keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, }, handlers) stop_on_error = if (is.numeric(options$error)) options$error else {36: if (options$error && options$include) withRestartList(expr, restarts)
0L
31: 37: else 2LdoWithOneRestart(return(expr), restart)withRestarts(with_handlers({
}, output_handler = knit_handlers(options$render, options)))32:
for (expr in tle$exprs) {42: withOneRestart(expr, restarts[[1L]]) ev <- withVisible(eval(expr, envir))
33: eng_r(options) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts[-nr])43:
}block_exec(params)34:
doWithOneRestart(return(expr), restart)
TRUE44: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)35: call_block(x)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
45:
38: process_group(group)36:
withRestartList(expr, restarts)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 37: withRestarts(with_handlers({ error = function(e) { for (expr in tle$exprs) { if (progress && is.function(pb$interrupt)) ev <- withVisible(eval(expr, envir)) pb$interrupt() watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) watcher$print_value(ev$value, ev$visible, envir) error <<- format(e) } })
evaluate::evaluate(...) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 38: 39: error = function(e) {evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, evaluate::evaluate(...) if (progress && is.function(pb$interrupt))
keep_message = if (is.numeric(options$message)) TRUE else options$message, 39: pb$interrupt() stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 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()) keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L error <<- format(e) stop_on_error = if (is.numeric(options$error)) options$error else { else 2L if (options$error && options$include) }), list(rlang_trace_top_env = knit_global())) }, output_handler = knit_handlers(options$render, options))
0L
else 2L40: 48: }, output_handler = knit_handlers(options$render, options))in_dir(input_dir(), expr)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 41: error = function(e) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, 40: if (progress && is.function(pb$interrupt)) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, pb$interrupt()in_dir(input_dir(), expr) stop_on_error = if (is.numeric(options$error)) options$error else {
if (is_R_CMD_build() || is_R_CMD_check()) 41: if (options$error && options$include) error <<- format(e) 0L }), list(rlang_trace_top_env = knit_global())), function(loc) { else 2L setwd(wd) }, output_handler = knit_handlers(options$render, options)))
in_input_dir(evaluate(code, envir = env, new_device = FALSE, write_utf8(res, output %n% stdout()) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, paste0("\nQuitting from ", loc, if (!is.null(error)) 42: paste0("\n", rule(), error, "\n", rule())) keep_message = if (is.numeric(options$message)) TRUE else options$message, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)eng_r(options) stop_on_error = if (is.numeric(options$error)) options$error else {
43: if (options$error && options$include) 49: block_exec(params) 0Lprocess_file(text, output) else 2L
50: }, output_handler = knit_handlers(options$render, options)))44:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)call_block(x)42:
51: eng_r(options)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 45:
output_dir = getwd(), ...)process_group(group)43:
46: 52: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
vweave_rmarkdown(...) error = function(e) {44:
if (progress && is.function(pb$interrupt)) 53: call_block(x)engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt()
45: process_group(group)54: if (is_R_CMD_build() || is_R_CMD_check()) doTryCatch(return(expr), name, parentenv, handler)
error <<- format(e)46: })withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
if (progress && is.function(pb$interrupt)) 47: pb$interrupt()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)55: }) error = function(e) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (progress && is.function(pb$interrupt))
pb$interrupt()56:
if (is_R_CMD_build() || is_R_CMD_check()) tryCatchList(expr, classes, parentenv, handlers) error <<- format(e)47:
}), list(rlang_trace_top_env = knit_global()))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
57: 48: tryCatch({ error = function(e) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), engine$weave(file, quiet = quiet, encoding = enc) error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) setwd(startdir) pb$interrupt() output <- find_vignette_product(name, by = "weave", engine = engine) if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() error <<- format(e) if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) texi2pdf(file = output, clean = FALSE, quiet = quiet) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) error <<- format(e) output <- find_vignette_product(name, by = "texi2pdf", write_utf8(res, output %n% stdout()) }), list(rlang_trace_top_env = knit_global())) engine = engine)
} paste0("\nQuitting from ", loc, if (!is.null(error)) outputs <- c(outputs, output) paste0("\n", rule(), error, "\n", rule()))48: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)}, error = function(e) {
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), thisOK <<- FALSE49: fails <<- c(fails, file)process_file(text, output) error = function(e) {
50: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
file, conditionMessage(e))) if (progress && is.function(pb$interrupt)) 51: })rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) output_dir = getwd(), ...)58: error <<- format(e)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
}), list(rlang_trace_top_env = knit_global())), function(loc) {52: setwd(wd)vweave_rmarkdown(...) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1DLhMx/fileabe51e9774bd.rds") write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error))
53: paste0("\n", rule(), error, "\n", rule()))An irrecoverable exception occurred. R is aborting now ...
engine$weave(file, quiet = quiet, encoding = enc)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
54:
doTryCatch(return(expr), name, parentenv, handler)49:
process_file(text, output)
55: 50: tryCatchOne(expr, names, parentenv, handlers[[1L]])knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
56: 51: tryCatchList(expr, classes, parentenv, handlers)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
57: 52: tryCatch({vweave_rmarkdown(...) engine$weave(file, quiet = quiet, encoding = enc)
53: setwd(startdir)engine$weave(file, quiet = quiet, encoding = enc) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 54: engine = engine)doTryCatch(return(expr), name, parentenv, handler)
}55: outputs <- c(outputs, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function(e) { thisOK <<- FALSE
fails <<- c(fails, file)56: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tryCatchList(expr, classes, parentenv, handlers) file, conditionMessage(e)))
})57:
tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)58: setwd(startdir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", output <- find_vignette_product(name, by = "weave", engine = engine) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1DLhMx/fileabe51e9774bd.rds")
if (!have.makefile && vignette_is_tex(output)) {An irrecoverable exception occurred. R is aborting now ...
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/Rtmp1DLhMx/fileabe51e9774bd.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