Last updated on 2026-10-20 01:50:21 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.66 | 225.50 | 229.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.23 | 229.99 | 232.22 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 191.21 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 5.00 | 137.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 4.09 | 205.01 | 209.10 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.20 | 209.21 | 212.41 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 6.00 | 132.00 | 138.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 7.00 | 158.00 | 165.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-10-20 06:11:10.937 R[39339:60889] 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() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
Traceback:
1: 36: withRestartList(expr, restarts)RowCumsum(valid)
37: 2: withRestarts(with_handlers({FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, for (expr in tle$exprs) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, ev <- withVisible(eval(expr, envir)) tieBreak = FALSE, verbose = verbose) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir) 3: } TRUESMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
tau = tau, theta = th, exclusionRadius = exclusionRadius, 38: embedded = embedded, validLib = validLib, noTime = noTime, evaluate::evaluate(...) ignoreNan = ignoreNan, backend = backend)
39: 4: ComputeError(predictions$Observations, predictions$Predictions)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { 5: if (options$error && options$include) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 0L knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, else 2L embedded = embedded, validLib = validLib, noTime = noTime, }, output_handler = knit_handlers(options$render, options))
ignoreNan = ignoreNan, backend = backend)$predictions)
40: 6: in_dir(input_dir(), expr)FUN(X[[i]], ...)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 7: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, lapply(X = S, FUN = FUN, ...) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 8: 0LdoTryCatch(return(expr), name, parentenv, handler) else 2L
}, output_handler = knit_handlers(options$render, options))) 9:
42: tryCatchOne(expr, names, parentenv, handlers[[1L]])eng_r(options)
10:
tryCatchList(expr, classes, parentenv, handlers)43: block_exec(params)
11: 44: tryCatch(expr, error = function(e) { call <- conditionCall(e)call_block(x) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 45: call <- sys.call(-4L)process_group(group) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L46: sm <- strsplit(conditionMessage(e), "\n")[[1L]]withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error = function(e) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (progress && is.function(pb$interrupt)) pb$interrupt() type = "b") if (w > LONG) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) prefix <- paste0(prefix, "\n ") }) }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")47: .Internal(seterrmessage(msg[1L]))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (!silent && isTRUE(getOption("show.error.messages"))) { if (progress && is.function(pb$interrupt)) cat(msg, file = outFile) pb$interrupt() .Internal(printDeferredWarnings()) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) invisible(structure(msg, class = "try-error", condition = e)) }), list(rlang_trace_top_env = knit_global()))})
48: 12: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), try(lapply(X = S, FUN = FUN, ...), silent = TRUE) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 13: error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) setwd(wd)
write_utf8(res, output %n% stdout())14: paste0("\nQuitting from ", loc, if (!is.null(error)) FUN(X[[i]], ...)
paste0("\n", rule(), error, "\n", rule()))15: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)lapply(seq_len(cores), inner.do)
49: 16: process_file(text, output)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 50: doTryCatch(return(expr), name, parentenv, handler)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: 18: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
52:
vweave_rmarkdown(...)19:
tryCatchList(expr, classes, parentenv, handlers)53:
Traceback:
engine$weave(file, quiet = quiet, encoding = enc) 1:
RowCumsum(valid)20: 54:
doTryCatch(return(expr), name, parentenv, handler)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 2:
mc.preschedule = TRUE), error = function(e) NULL)
Traceback:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 55: 1: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 21: RowCumsum(valid)tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepApply(theta, worker, numProcess) tieBreak = FALSE, verbose = verbose)
22: 56: unlist(SweepApply(theta, worker, numProcess))
3: tryCatchList(expr, classes, parentenv, handlers) 2: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
23: 57: tau = tau, theta = th, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, embedded = embedded, validLib = validLib, noTime = noTime, tryCatch({PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", engine$weave(file, quiet = quiet, encoding = enc) ignoreNan = ignoreNan, backend = backend) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", tieBreak = FALSE, verbose = verbose) setwd(startdir) E = E, showPlot = TRUE)
output <- find_vignette_product(name, by = "weave", engine = engine)
4:
ComputeError(predictions$Observations, predictions$Predictions)
if (!have.makefile && vignette_is_tex(output)) {24: 3: 5: texi2pdf(file = output, clean = FALSE, quiet = quiet)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tau = tau, theta = th, exclusionRadius = exclusionRadius, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, output <- find_vignette_product(name, by = "texi2pdf", eval(expr, envir) engine = engine) ignoreNan = ignoreNan, backend = backend)$predictions) } outputs <- c(outputs, output)
}, error = function(e) {25: thisOK <<- FALSE 6: embedded = embedded, validLib = validLib, noTime = noTime, fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", eval(expr, envir)FUN(X[[i]], ...) ignoreNan = ignoreNan, backend = backend)
file, conditionMessage(e))) 7:
4: 26: })ComputeError(predictions$Observations, predictions$Predictions)
lapply(X = S, FUN = FUN, ...)58: withVisible(eval(expr, envir))
8: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", doTryCatch(return(expr), name, parentenv, handler) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1Vd8mU/file888323de0fd0.rds")27: 5: withCallingHandlers(code, error = function (e)
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, An irrecoverable exception occurred. R is aborting now ...
9: rlang::entrace(e), message = function (cnd) tryCatchOne(expr, names, parentenv, handlers[[1L]]) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, {10: ignoreNan = ignoreNan, backend = backend)$predictions)tryCatchList(expr, classes, parentenv, handlers)
watcher$capture_plot_and_output()
6: 11: if (on_message$capture) {tryCatch(expr, error = function(e) {FUN(X[[i]], ...) watcher$push(cnd) call <- conditionCall(e)
} if (!is.null(call)) { if (on_message$silence) { if (identical(call[[1L]], quote(doTryCatch))) invokeRestart("muffleMessage") call <- sys.call(-4L) } 7: }, warning = function (cnd) lapply(X = S, FUN = FUN, ...){ dcall <- deparse(call, nlines = 1L) if (getOption("warn") >= 2 || getOption("warn") < 0) { prefix <- paste("Error in", dcall, ": ")
return() 8: LONG <- 75L }doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
sm <- strsplit(conditionMessage(e), "\n")[[1L]] 9: if (on_warning$capture) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cnd <- sanitize_call(cnd) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 10: watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) type = "b")
} if (w > LONG) 11: prefix <- paste0(prefix, "\n ")tryCatch(expr, error = function(e) { if (on_warning$silence) { } call <- conditionCall(e) else prefix <- "Error : " invokeRestart("muffleWarning") if (!is.null(call)) { msg <- paste0(prefix, conditionMessage(e), "\n") if (identical(call[[1L]], quote(doTryCatch))) .Internal(seterrmessage(msg[1L])) } call <- sys.call(-4L)}, error = function (cnd) if (!silent && isTRUE(getOption("show.error.messages"))) {{ dcall <- deparse(call, nlines = 1L) watcher$capture_plot_and_output() cat(msg, file = outFile) prefix <- paste("Error in", dcall, ": ") cnd <- sanitize_call(cnd) LONG <- 75L .Internal(printDeferredWarnings()) sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$push(cnd) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } if (is.na(w)) invisible(structure(msg, class = "try-error", condition = e)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }) type = "b") switch(on_error, continue = invokeRestart("eval_continue"),
if (w > LONG) stop = invokeRestart("eval_stop"), error = NULL)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) prefix <- paste0(prefix, "\n ")}) }
28: 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))eval(call)
29: else prefix <- "Error : "eval(call) msg <- paste0(prefix, conditionMessage(e), "\n")14:
.Internal(seterrmessage(msg[1L]))30: FUN(X[[i]], ...) if (!silent && isTRUE(getOption("show.error.messages"))) {with_handlers({ cat(msg, file = outFile) for (expr in tle$exprs) { .Internal(printDeferredWarnings())
} ev <- withVisible(eval(expr, envir)) invisible(structure(msg, class = "try-error", condition = e))15: })lapply(seq_len(cores), inner.do) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)12: 16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) }
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)13: TRUE
}, handlers)17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
31: doTryCatch(return(expr), name, parentenv, handler)14:
doWithOneRestart(return(expr), restart)FUN(X[[i]], ...)
32: 15: withOneRestart(expr, restarts[[1L]])18: lapply(seq_len(cores), inner.do)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
33:
16: 19: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
17: 34: 20: doWithOneRestart(return(expr), restart)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, doTryCatch(return(expr), name, parentenv, handler)
mc.preschedule = TRUE), error = function(e) NULL)35:
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
21:
SweepApply(theta, worker, numProcess)19: 36: tryCatchList(expr, classes, parentenv, handlers)withRestartList(expr, restarts)
22:
20: unlist(SweepApply(theta, worker, numProcess))37: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, withRestarts(with_handlers({ mc.preschedule = TRUE), error = function(e) NULL) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))
21: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", watcher$capture_plot_and_output()SweepApply(theta, worker, numProcess) target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
watcher$print_value(ev$value, ev$visible, envir) E = E, showPlot = TRUE)22: }
unlist(SweepApply(theta, worker, numProcess)) TRUE24:
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)eval(expr, envir)
23: 38: evaluate::evaluate(...)
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 39: 25: 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, eval(expr, envir) stop_on_error = if (is.numeric(options$error)) options$error else {
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", if (options$error && options$include) E = E, showPlot = TRUE) 0L26:
withVisible(eval(expr, envir)) else 2L24: }, output_handler = knit_handlers(options$render, options))
eval(expr, envir)
27:
withCallingHandlers(code, error = function (e) 40: 25: rlang::entrace(e), message = function (cnd) in_dir(input_dir(), expr)eval(expr, envir)
{ watcher$capture_plot_and_output()41: if (on_message$capture) {26: in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$push(cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, withVisible(eval(expr, envir)) 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) 27: 0L if (on_message$silence) {withCallingHandlers(code, error = function (e) invokeRestart("muffleMessage") else 2Lrlang::entrace(e), message = function (cnd) }}, warning = function (cnd) {{ if (getOption("warn") >= 2 || getOption("warn") < 0) { }, output_handler = knit_handlers(options$render, options))) return()
watcher$capture_plot_and_output() }42: if (on_message$capture) { watcher$capture_plot_and_output() if (on_warning$capture) { watcher$push(cnd)eng_r(options) cnd <- sanitize_call(cnd) } if (on_message$silence) {
watcher$push(cnd) invokeRestart("muffleMessage") }43: } if (on_warning$silence) {block_exec(params) invokeRestart("muffleWarning")}, warning = function (cnd)
{ } if (getOption("warn") >= 2 || getOption("warn") < 0) {}, error = function (cnd) 44: return(){ }call_block(x) watcher$capture_plot_and_output()
watcher$capture_plot_and_output()45: if (on_warning$capture) {process_group(group) cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd)
watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), 46: stop = invokeRestart("eval_stop"), error = NULL) }}) if (on_warning$silence) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
invokeRestart("muffleWarning") error = function(e) {28: if (progress && is.function(pb$interrupt)) eval(call) } pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) }, error = function (cnd) error <<- format(e){ watcher$capture_plot_and_output() })29: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
eval(call)
47: 28:
eval(call)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
29: eval(call)30:
30: error = function(e) {with_handlers({with_handlers({ if (progress && is.function(pb$interrupt)) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$print_value(ev$value, ev$visible, envir) } TRUE watcher$capture_plot_and_output()}, handlers) }), list(rlang_trace_top_env = knit_global()))
watcher$print_value(ev$value, ev$visible, envir)31: 48: }doWithOneRestart(return(expr), restart)
TRUExfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, handlers)32:
withOneRestart(expr, restarts[[1L]])31: error = function(e) {
doWithOneRestart(return(expr), restart)
if (progress && is.function(pb$interrupt)) 32: 33: pb$interrupt()withOneRestart(expr, restarts[[1L]]) if (is_R_CMD_build() || is_R_CMD_check()) withRestartList(expr, restarts[-nr]) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {
33: setwd(wd)34: withRestartList(expr, restarts[-nr]) write_utf8(res, output %n% stdout())doWithOneRestart(return(expr), restart)
35: paste0("\nQuitting from ", loc, if (!is.null(error)) 34: doWithOneRestart(return(expr), restart) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
49: 36: 36: withRestartList(expr, restarts)withRestartList(expr, restarts)process_file(text, output)
50: 37: 37: withRestarts(with_handlers({knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) for (expr in tle$exprs) {
withRestarts(with_handlers({ ev <- withVisible(eval(expr, envir))51: for (expr in tle$exprs) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)52: watcher$print_value(ev$value, ev$visible, envir)vweave_rmarkdown(...) } } TRUE
TRUE53: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)engine$weave(file, quiet = quiet, encoding = enc)38:
54: 38: evaluate::evaluate(...)doTryCatch(return(expr), name, parentenv, handler)
evaluate::evaluate(...)
39: 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 55: keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {tryCatchOne(expr, names, parentenv, handlers[[1L]]) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
if (options$error && options$include) 56: 0LtryCatchList(expr, classes, parentenv, handlers) 0L else 2L
else 2L57: }, output_handler = knit_handlers(options$render, options))tryCatch({ }, output_handler = knit_handlers(options$render, options))
engine$weave(file, quiet = quiet, encoding = enc)40: in_dir(input_dir(), expr)40: setwd(startdir)in_dir(input_dir(), expr)
41: output <- find_vignette_product(name, by = "weave", engine = engine)in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (!have.makefile && vignette_is_tex(output)) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 41: engine = engine) 0Lin_input_dir(evaluate(code, envir = env, new_device = FALSE, } else 2L outputs <- c(outputs, output) }, output_handler = knit_handlers(options$render, options))) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
}, error = function(e) {42: keep_message = if (is.numeric(options$message)) TRUE else options$message, eng_r(options) thisOK <<- FALSE fails <<- c(fails, file) stop_on_error = if (is.numeric(options$error)) options$error else { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (options$error && options$include)
file, conditionMessage(e)))43: 0L}) else 2L
}, output_handler = knit_handlers(options$render, options)))block_exec(params)58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 42: 44: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1Vd8mU/file888323de0fd0.rds")eng_r(options)call_block(x)
An irrecoverable exception occurred. R is aborting now ...
43: 45: process_group(group)block_exec(params)
44: 46: call_block(x)
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: error = function(e) {process_group(group) if (progress && is.function(pb$interrupt))
pb$interrupt()46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(e) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 47: error <<- format(e) })with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {47: if (progress && is.function(pb$interrupt)) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))48:
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) if (progress && is.function(pb$interrupt)) pb$interrupt() pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) setwd(wd) write_utf8(res, output %n% stdout()) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) paste0("\nQuitting from ", loc, if (!is.null(error)) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: 49: process_file(text, output)
process_file(text, output)50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: 51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
52: 51: vweave_rmarkdown(...)
53: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), engine$weave(file, quiet = quiet, encoding = enc) output_dir = getwd(), ...)
54: doTryCatch(return(expr), name, parentenv, handler)52:
vweave_rmarkdown(...)55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])53:
engine$weave(file, quiet = quiet, encoding = enc)
56: 54: tryCatchList(expr, classes, parentenv, handlers)doTryCatch(return(expr), name, parentenv, handler)
57: 55: tryCatch({tryCatchOne(expr, names, parentenv, handlers[[1L]]) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)56: output <- find_vignette_product(name, by = "weave", engine = engine)tryCatchList(expr, classes, parentenv, handlers) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)57: output <- find_vignette_product(name, by = "texi2pdf", tryCatch({ engine = engine) engine$weave(file, quiet = quiet, encoding = enc) } setwd(startdir) outputs <- c(outputs, output) output <- find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) thisOK <<- FALSE output <- find_vignette_product(name, by = "texi2pdf", fails <<- c(fails, file) engine = engine) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }}) outputs <- c(outputs, output)}, error = function(e) {
thisOK <<- FALSE58: fails <<- c(fails, file)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp1Vd8mU/file888323de0fd0.rds") file, conditionMessage(e)))
})An irrecoverable exception occurred. R is aborting now ...
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/Rtmp1Vd8mU/file888323de0fd0.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