Last updated on 2026-11-02 04:55:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.71 | 227.73 | 231.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.49 | 242.92 | 245.41 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 190.30 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.82 | 207.25 | 211.07 | 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 | 40.00 | 42.00 | 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 | 159.00 | 165.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-02 15:23:35.204 R[43017:65659] 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$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4:
Traceback:
ComputeError(predictions$Observations, predictions$Predictions) 1:
RowCumsum(valid) 5:
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tieBreak = FALSE, verbose = verbose) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 6: tau = tau, theta = th, exclusionRadius = exclusionRadius, FUN(X[[i]], ...) embedded = embedded, validLib = validLib, noTime = noTime,
7: ignoreNan = ignoreNan, backend = backend)lapply(X = S, FUN = FUN, ...)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 8: doTryCatch(return(expr), name, parentenv, handler) ignoreNan = ignoreNan, backend = backend)$predictions)
9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: FUN(X[[i]], ...)
10:
7: lapply(X = S, FUN = FUN, ...)tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) 8: if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) if (identical(call[[1L]], quote(doTryCatch)))
9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")10: LONG <- 75LtryCatchList(expr, classes, parentenv, handlers)
sm <- strsplit(conditionMessage(e), "\n")[[1L]]11: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") call <- conditionCall(e) if (!is.null(call)) { if (w > LONG) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste0(prefix, "\n ") } call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- paste0(prefix, conditionMessage(e), "\n") sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(seterrmessage(msg[1L])) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!silent && isTRUE(getOption("show.error.messages"))) { if (is.na(w)) cat(msg, file = outFile) .Internal(printDeferredWarnings()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], } type = "b") invisible(structure(msg, class = "try-error", condition = e)) if (w > LONG) prefix <- paste0(prefix, "\n ") }}) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")12: .Internal(seterrmessage(msg[1L]))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) .Internal(printDeferredWarnings())13: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invisible(structure(msg, class = "try-error", condition = e))})
12: 14: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)FUN(X[[i]], ...)
13: 15: lapply(seq_len(cores), inner.do)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)14:
Traceback:
FUN(X[[i]], ...)17: 1:
doTryCatch(return(expr), name, parentenv, handler)RowCumsum(valid)15:
lapply(seq_len(cores), inner.do)
18: 2: 16: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]])parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
19: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatchList(expr, classes, parentenv, handlers)17: tieBreak = FALSE, verbose = verbose)
doTryCatch(return(expr), name, parentenv, handler)
20:
3: 18: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatchOne(expr, names, parentenv, handlers[[1L]]) embedded = embedded, validLib = validLib, noTime = noTime, mc.preschedule = TRUE), error = function(e) NULL)
ignoreNan = ignoreNan, backend = backend)
21: 19: 4: SweepApply(theta, worker, numProcess)ComputeError(predictions$Observations, predictions$Predictions)
22: unlist(SweepApply(theta, worker, numProcess)) 5: tryCatchList(expr, classes, parentenv, handlers)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
23: 20: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", mc.preschedule = TRUE), error = function(e) NULL) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE) embedded = embedded, validLib = validLib, noTime = noTime, 21:
ignoreNan = ignoreNan, backend = backend)$predictions)24: SweepApply(theta, worker, numProcess)eval(expr, envir)
6: 22:
FUN(X[[i]], ...)25: unlist(SweepApply(theta, worker, numProcess))
eval(expr, envir) 7:
lapply(X = S, FUN = FUN, ...)23: 26:
withVisible(eval(expr, envir))PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 8:
doTryCatch(return(expr), name, parentenv, handler)27:
withCallingHandlers(code, error = function (e) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", rlang::entrace(e), message = function (cnd) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]){
E = E, showPlot = TRUE) watcher$capture_plot_and_output()10:
tryCatchList(expr, classes, parentenv, handlers)24: if (on_message$capture) {
eval(expr, envir)11: watcher$push(cnd) }
tryCatch(expr, error = function(e) { if (on_message$silence) {25: invokeRestart("muffleMessage") call <- conditionCall(e) }eval(expr, envir) if (!is.null(call)) {}, warning = function (cnd)
if (identical(call[[1L]], quote(doTryCatch))) 26: withVisible(eval(expr, envir)){
call <- sys.call(-4L)27: if (getOption("warn") >= 2 || getOption("warn") < 0) { dcall <- deparse(call, nlines = 1L)withCallingHandlers(code, error = function (e) prefix <- paste("Error in", dcall, ": ") return() LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]]rlang::entrace(e), message = function (cnd) watcher$capture_plot_and_output(){ w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (on_warning$capture) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") watcher$capture_plot_and_output() if (on_message$capture) { if (w > LONG) cnd <- sanitize_call(cnd) watcher$push(cnd) prefix <- paste0(prefix, "\n ") watcher$push(cnd) } } } if (on_warning$silence) { else prefix <- "Error : " if (on_message$silence) { invokeRestart("muffleWarning") } msg <- paste0(prefix, conditionMessage(e), "\n") invokeRestart("muffleMessage")}, error = function (cnd) .Internal(seterrmessage(msg[1L])) }{ if (!silent && isTRUE(getOption("show.error.messages"))) {}, warning = function (cnd) watcher$capture_plot_and_output(){ cnd <- sanitize_call(cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd) cat(msg, file = outFile) .Internal(printDeferredWarnings()) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) return()}) invisible(structure(msg, class = "try-error", condition = e))
}})28:
watcher$capture_plot_and_output()eval(call) if (on_warning$capture) {
12: 29: cnd <- sanitize_call(cnd)eval(call)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) watcher$push(cnd)
} if (on_warning$silence) {
13: invokeRestart("muffleWarning")sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))30:
with_handlers({ } for (expr in tle$exprs) {14: }, error = function (cnd) FUN(X[[i]], ...) ev <- withVisible(eval(expr, envir)){ watcher$capture_plot_and_output()
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)15: cnd <- sanitize_call(cnd) }lapply(seq_len(cores), inner.do) TRUE}, handlers) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 31:
stop = invokeRestart("eval_stop"), error = NULL)doWithOneRestart(return(expr), restart)
16: 32: })parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withOneRestart(expr, restarts[[1L]])
28: eval(call)33: 17: withRestartList(expr, restarts[-nr])doTryCatch(return(expr), name, parentenv, handler)
34:
18: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
eval(call)35: 19:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])30:
tryCatchList(expr, classes, parentenv, handlers)36: with_handlers({
for (expr in tle$exprs) {20: withRestartList(expr, restarts) ev <- withVisible(eval(expr, envir))tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL) watcher$capture_plot_and_output()
37: watcher$print_value(ev$value, ev$visible, envir)21: withRestarts(with_handlers({ }SweepApply(theta, worker, numProcess) TRUE
22: }, handlers)unlist(SweepApply(theta, worker, numProcess)) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))23:
watcher$capture_plot_and_output()PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 31: watcher$print_value(ev$value, ev$visible, envir) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", doWithOneRestart(return(expr), restart) } E = E, showPlot = TRUE)
24: TRUEeval(expr, envir)32:
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)withOneRestart(expr, restarts[[1L]])25:
eval(expr, envir)
38: 33: 26: withRestartList(expr, restarts[-nr])evaluate::evaluate(...)withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) 34: rlang::entrace(e), message = function (cnd) doWithOneRestart(return(expr), restart)39: {
35: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_message$capture) { keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd)36: if (options$error && options$include) }withRestartList(expr, restarts) if (on_message$silence) {
invokeRestart("muffleMessage") 0L37: }withRestarts(with_handlers({}, warning = function (cnd) else 2L for (expr in tle$exprs) { }, output_handler = knit_handlers(options$render, options)){ ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$print_value(ev$value, ev$visible, envir) return()
} TRUE }}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)40:
watcher$capture_plot_and_output()in_dir(input_dir(), expr)
38: evaluate::evaluate(...) if (on_warning$capture) {
41: cnd <- sanitize_call(cnd)in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$push(cnd)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 (on_warning$silence) { if (options$error && options$include) keep_message = if (is.numeric(options$message)) TRUE else options$message, invokeRestart("muffleWarning") stop_on_error = if (is.numeric(options$error)) options$error else {
Traceback:
} 0L else 2L if (options$error && options$include) 1: }, error = function (cnd) 0L }, output_handler = knit_handlers(options$render, options)))RowCumsum(valid){ else 2L
watcher$capture_plot_and_output() }, output_handler = knit_handlers(options$render, options)) cnd <- sanitize_call(cnd)42: watcher$push(cnd) 2: switch(on_error, continue = invokeRestart("eval_continue"), eng_r(options)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, stop = invokeRestart("eval_stop"), error = NULL) tieBreak = FALSE, verbose = verbose)})43:
40: 3:
in_dir(input_dir(), expr)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 28: block_exec(params)
eval(call)41: tau = tau, theta = th, exclusionRadius = exclusionRadius,
in_input_dir(evaluate(code, envir = env, new_device = FALSE, embedded = embedded, validLib = validLib, noTime = noTime, 44: 29: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eval(call)call_block(x) keep_message = if (is.numeric(options$message)) TRUE else options$message,
30: stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend)45: with_handlers({ if (options$error && options$include) for (expr in tle$exprs) {
0L ev <- withVisible(eval(expr, envir)) 4: process_group(group) else 2L watcher$capture_plot_and_output()ComputeError(predictions$Observations, predictions$Predictions)
watcher$print_value(ev$value, ev$visible, envir)46:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } }, output_handler = knit_handlers(options$render, options))) error = function(e) { TRUE if (progress && is.function(pb$interrupt)) 5:
}, handlers)42: eng_r(options) pb$interrupt()SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 31: embedded = embedded, validLib = validLib, noTime = noTime, 43: })doWithOneRestart(return(expr), restart)block_exec(params)
ignoreNan = ignoreNan, backend = backend)$predictions)
32: 6:
47: FUN(X[[i]], ...)withOneRestart(expr, restarts[[1L]])44:
call_block(x)
7:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 33: lapply(X = S, FUN = FUN, ...)45: withRestartList(expr, restarts[-nr])
process_group(group)34:
8: doWithOneRestart(return(expr), restart)46: error = function(e) {
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), doTryCatch(return(expr), name, parentenv, handler)35: error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt))
pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 9: if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)tryCatchOne(expr, names, parentenv, handlers[[1L]])36: withRestartList(expr, restarts) }), list(rlang_trace_top_env = knit_global()))
error <<- format(e)
37: 10: 48: tryCatchList(expr, classes, parentenv, handlers)withRestarts(with_handlers({ for (expr in tle$exprs) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) { ev <- withVisible(eval(expr, envir))
11: watcher$capture_plot_and_output()47: if (progress && is.function(pb$interrupt)) watcher$print_value(ev$value, ev$visible, envir)tryCatch(expr, error = function(e) { pb$interrupt() } call <- conditionCall(e)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), TRUE if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { if (!is.null(call)) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) error <<- format(e) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
38: pb$interrupt() if (identical(call[[1L]], quote(doTryCatch))) setwd(wd)evaluate::evaluate(...) if (is_R_CMD_build() || is_R_CMD_check()) write_utf8(res, output %n% stdout()) call <- sys.call(-4L) error <<- format(e) paste0("\nQuitting from ", loc, if (!is.null(error))
}), list(rlang_trace_top_env = knit_global()))
39: paste0("\n", rule(), error, "\n", rule()))evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 48: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) keep_message = if (is.numeric(options$message)) TRUE else options$message, xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") stop_on_error = if (is.numeric(options$error)) options$error else { LONG <- 75L49: sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (options$error && options$include) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")process_file(text, output) 0L
if (is.na(w)) error = function(e) {50: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") else 2L if (w > LONG) if (progress && is.function(pb$interrupt)) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }, output_handler = knit_handlers(options$render, options)) prefix <- paste0(prefix, "\n ")
} pb$interrupt()
40: 51: else prefix <- "Error : " if (is_R_CMD_build() || is_R_CMD_check()) in_dir(input_dir(), expr)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), msg <- paste0(prefix, conditionMessage(e), "\n") error <<- format(e) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {41: }), list(rlang_trace_top_env = knit_global())), function(loc) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, setwd(wd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, cat(msg, file = outFile) stop_on_error = if (is.numeric(options$error)) options$error else { write_utf8(res, output %n% stdout()) .Internal(printDeferredWarnings()) paste0("\nQuitting from ", loc, if (!is.null(error)) if (options$error && options$include) paste0("\n", rule(), error, "\n", rule())) output_dir = getwd(), ...)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 0L }
invisible(structure(msg, class = "try-error", condition = e)) else 2L52: }) }, output_handler = knit_handlers(options$render, options)))49:
process_file(text, output)
vweave_rmarkdown(...)
42: 12: eng_r(options)50: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
53: 13:
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))engine$weave(file, quiet = quiet, encoding = enc) output_dir = getwd(), ...)
43: 54: 14: block_exec(params)52: FUN(X[[i]], ...)vweave_rmarkdown(...)
doTryCatch(return(expr), name, parentenv, handler)
44:
53: 15: call_block(x)
engine$weave(file, quiet = quiet, encoding = enc)lapply(seq_len(cores), inner.do)
55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: 16:
54: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)process_group(group)56: tryCatchList(expr, classes, parentenv, handlers)
doTryCatch(return(expr), name, parentenv, handler)46:
55: 57: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatchOne(expr, names, parentenv, handlers[[1L]])17: tryCatch({ error = function(e) {
doTryCatch(return(expr), name, parentenv, handler) engine$weave(file, quiet = quiet, encoding = enc)
if (progress && is.function(pb$interrupt)) 56: pb$interrupt()tryCatchList(expr, classes, parentenv, handlers) if (is_R_CMD_build() || is_R_CMD_check()) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)18: error <<- format(e)57: if (!have.makefile && vignette_is_tex(output)) { }) texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch({ output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)19: engine$weave(file, quiet = quiet, encoding = enc) }tryCatchList(expr, classes, parentenv, handlers) setwd(startdir) outputs <- c(outputs, output)47: output <- find_vignette_product(name, by = "weave", engine = engine)
20: }, error = function(e) { if (!have.makefile && vignette_is_tex(output)) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), thisOK <<- FALSEtryCatch(parallel::mclapply(values, worker, mc.cores = cores, fails <<- c(fails, file) texi2pdf(file = output, clean = FALSE, quiet = quiet) error = function(e) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", output <- find_vignette_product(name, by = "texi2pdf", engine = engine) file, conditionMessage(e))) mc.preschedule = TRUE), error = function(e) NULL) } if (progress && is.function(pb$interrupt)) }) outputs <- c(outputs, output) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) }, error = function(e) {
thisOK <<- FALSE
21: fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", error <<- format(e)58: }), list(rlang_trace_top_env = knit_global())) file, conditionMessage(e)))
SweepApply(theta, worker, numProcess)48: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpfwTCUn/file98f71974a9a1.rds") error = function(e) {
if (progress && is.function(pb$interrupt)) 58: 22:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) An irrecoverable exception occurred. R is aborting now ...
error <<- format(e) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpfwTCUn/file98f71974a9a1.rds")unlist(SweepApply(theta, worker, numProcess)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)23:
write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", paste0("\n", rule(), error, "\n", rule())) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) E = E, showPlot = TRUE)
49: An irrecoverable exception occurred. R is aborting now ...
24: process_file(text, output)eval(expr, envir)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)25: eval(expr, envir)
51: 26: withVisible(eval(expr, envir))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: 27: withCallingHandlers(code, error = function (e) vweave_rmarkdown(...)rlang::entrace(e), message = function (cnd)
{53: watcher$capture_plot_and_output()engine$weave(file, quiet = quiet, encoding = enc) if (on_message$capture) { watcher$push(cnd)
} if (on_message$silence) {54: invokeRestart("muffleMessage")doTryCatch(return(expr), name, parentenv, handler) }}, warning = function (cnd)
55: { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()tryCatchOne(expr, names, parentenv, handlers[[1L]]) } watcher$capture_plot_and_output()
if (on_warning$capture) {56: tryCatchList(expr, classes, parentenv, handlers) cnd <- sanitize_call(cnd)
watcher$push(cnd)57: }tryCatch({ if (on_warning$silence) { engine$weave(file, quiet = quiet, encoding = enc) invokeRestart("muffleWarning") } setwd(startdir)}, error = function (cnd) { output <- find_vignette_product(name, by = "weave", engine = engine) watcher$capture_plot_and_output() if (!have.makefile && vignette_is_tex(output)) { cnd <- sanitize_call(cnd) texi2pdf(file = output, clean = FALSE, quiet = quiet) watcher$push(cnd) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) outputs <- c(outputs, output)})}, error = function(e) { thisOK <<- FALSE
fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 28: file, conditionMessage(e)))eval(call)
29: })eval(call)
30:
with_handlers({58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", for (expr in tle$exprs) { skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpfwTCUn/file98f71974a9a1.rds") ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)An irrecoverable exception occurred. R is aborting now ...
} TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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/RtmpfwTCUn/file98f71974a9a1.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