Last updated on 2026-11-03 22:58:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.59 | 220.83 | 224.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.58 | 217.99 | 220.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.37 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 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 | 44.00 | 46.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 155.00 | 161.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-04 05:53:25.633 R[43203:67298] 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:
Traceback:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 1:
RowCumsum(valid)14:
FUN(X[[i]], ...) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 15: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, lapply(seq_len(cores), inner.do) tieBreak = FALSE, verbose = verbose)
16: 3: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 17: embedded = embedded, validLib = validLib, noTime = noTime, doTryCatch(return(expr), name, parentenv, handler) ignoreNan = ignoreNan, backend = backend)
18: 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])ComputeError(predictions$Observations, predictions$Predictions)
19: 5: tryCatchList(expr, classes, parentenv, handlers)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 20: embedded = embedded, validLib = validLib, noTime = noTime, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, ignoreNan = ignoreNan, backend = backend)$predictions)
mc.preschedule = TRUE), error = function(e) NULL) 6:
FUN(X[[i]], ...)21:
7: lapply(X = S, FUN = FUN, ...)SweepApply(theta, worker, numProcess)
8: 22: unlist(SweepApply(theta, worker, numProcess))doTryCatch(return(expr), name, parentenv, handler)
9: 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 10: E = E, showPlot = TRUE)tryCatchList(expr, classes, parentenv, handlers)
24: 11: eval(expr, envir)tryCatch(expr, error = function(e) {
call <- conditionCall(e)25: if (!is.null(call)) {eval(expr, envir) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)26: dcall <- deparse(call, nlines = 1L)withVisible(eval(expr, envir)) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L27: sm <- strsplit(conditionMessage(e), "\n")[[1L]]withCallingHandlers(code, error = function (e) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")rlang::entrace(e), message = function (cnd) if (is.na(w)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$capture_plot_and_output() type = "b") if (on_message$capture) { if (w > LONG) watcher$push(cnd) prefix <- paste0(prefix, "\n ") } } if (on_message$silence) { else prefix <- "Error : " invokeRestart("muffleMessage") msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {}, warning = function (cnd) cat(msg, file = outFile){ .Internal(printDeferredWarnings()) if (getOption("warn") >= 2 || getOption("warn") < 0) { } return() invisible(structure(msg, class = "try-error", condition = e)) }}) watcher$capture_plot_and_output()
if (on_warning$capture) {12: cnd <- sanitize_call(cnd)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) watcher$push(cnd)
}13: if (on_warning$silence) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) invokeRestart("muffleWarning") }
}, error = function (cnd) 14: {FUN(X[[i]], ...)
Traceback:
watcher$capture_plot_and_output() 1: cnd <- sanitize_call(cnd)RowCumsum(valid)
watcher$push(cnd) 2: 15: switch(on_error, continue = invokeRestart("eval_continue"), FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, lapply(seq_len(cores), inner.do) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, stop = invokeRestart("eval_stop"), error = NULL) tieBreak = FALSE, verbose = verbose)
})
16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 28: tau = tau, theta = th, exclusionRadius = exclusionRadius, 17: eval(call) embedded = embedded, validLib = validLib, noTime = noTime, doTryCatch(return(expr), name, parentenv, handler)
ignoreNan = ignoreNan, backend = backend)
29:
18: eval(call)tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: 30:
ComputeError(predictions$Observations, predictions$Predictions)19: with_handlers({tryCatchList(expr, classes, parentenv, handlers)
for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) 5: watcher$capture_plot_and_output()20: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$print_value(ev$value, ev$visible, envir) mc.preschedule = TRUE), error = function(e) NULL)
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, }21: TRUE embedded = embedded, validLib = validLib, noTime = noTime, SweepApply(theta, worker, numProcess) ignoreNan = ignoreNan, backend = backend)$predictions)
}, handlers)22:
6:
unlist(SweepApply(theta, worker, numProcess))FUN(X[[i]], ...)31:
23: doWithOneRestart(return(expr), restart) 7: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", lapply(X = S, FUN = FUN, ...)
32: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 8: E = E, showPlot = TRUE)withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler)
33: 9: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])withRestartList(expr, restarts[-nr])eval(expr, envir)
10: 25: 34: tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
eval(expr, envir)
35: 11: 26: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatch(expr, error = function(e) {
call <- conditionCall(e)36: withVisible(eval(expr, envir))withRestartList(expr, restarts) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 27: 37: call <- sys.call(-4L)withCallingHandlers(code, error = function (e) withRestarts(with_handlers({rlang::entrace(e), message = function (cnd) for (expr in tle$exprs) { dcall <- deparse(call, nlines = 1L) ev <- withVisible(eval(expr, envir)){ watcher$capture_plot_and_output() watcher$capture_plot_and_output() prefix <- paste("Error in", dcall, ": ") if (on_message$capture) { LONG <- 75L watcher$print_value(ev$value, ev$visible, envir) watcher$push(cnd) sm <- strsplit(conditionMessage(e), "\n")[[1L]] } TRUE } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (on_message$silence) { if (is.na(w))
invokeRestart("muffleMessage") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 38: type = "b") }evaluate::evaluate(...) if (w > LONG)
prefix <- paste0(prefix, "\n ")39: }, warning = function (cnd) }{ else prefix <- "Error : " if (getOption("warn") >= 2 || getOption("warn") < 0) { return() msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) watcher$capture_plot_and_output()evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (!silent && isTRUE(getOption("show.error.messages"))) { if (on_warning$capture) { keep_message = if (is.numeric(options$message)) TRUE else options$message, cat(msg, file = outFile) cnd <- sanitize_call(cnd) stop_on_error = if (is.numeric(options$error)) options$error else { watcher$push(cnd) if (options$error && options$include) .Internal(printDeferredWarnings()) } 0L } if (on_warning$silence) { else 2L invokeRestart("muffleWarning") }, output_handler = knit_handlers(options$render, options)) invisible(structure(msg, class = "try-error", condition = e))
}40: })in_dir(input_dir(), expr)}, error = function (cnd)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, {12: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, try(lapply(X = S, FUN = FUN, ...), silent = TRUE) watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { cnd <- sanitize_call(cnd) if (options$error && options$include) 13: watcher$push(cnd) 0LsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else 2L switch(on_error, continue = invokeRestart("eval_continue"),
14: stop = invokeRestart("eval_stop"), error = NULL) }, output_handler = knit_handlers(options$render, options)))FUN(X[[i]], ...)})
42:
28: eng_r(options)15:
eval(call)lapply(seq_len(cores), inner.do)
43: 29:
eval(call)16: block_exec(params)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
30:
with_handlers({44: 17: for (expr in tle$exprs) {call_block(x)doTryCatch(return(expr), name, parentenv, handler)
ev <- withVisible(eval(expr, envir))45:
process_group(group)18: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]])
watcher$print_value(ev$value, ev$visible, envir)
}19: 46: tryCatchList(expr, classes, parentenv, handlers)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), TRUE
error = function(e) {20: if (progress && is.function(pb$interrupt)) }, handlers) pb$interrupt()tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
if (is_R_CMD_build() || is_R_CMD_check()) mc.preschedule = TRUE), error = function(e) NULL) error <<- format(e)31:
})21: doWithOneRestart(return(expr), restart)
SweepApply(theta, worker, numProcess)47:
32: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 22: withOneRestart(expr, restarts[[1L]]) error = function(e) {unlist(SweepApply(theta, worker, numProcess))
if (progress && is.function(pb$interrupt)) 33:
withRestartList(expr, restarts[-nr]) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 34: error <<- format(e) }), list(rlang_trace_top_env = knit_global()))23: doWithOneRestart(return(expr), restart)
48: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 35: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", error = function(e) { E = E, showPlot = TRUE) if (progress && is.function(pb$interrupt)) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
pb$interrupt()24: if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)eval(expr, envir) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)36: write_utf8(res, output %n% stdout())
withRestartList(expr, restarts)25:
eval(expr, envir) paste0("\nQuitting from ", loc, if (!is.null(error))
37: 26: paste0("\n", rule(), error, "\n", rule()))withRestarts(with_handlers({}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withVisible(eval(expr, envir)) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))27: 49: watcher$capture_plot_and_output()withCallingHandlers(code, error = function (e) watcher$print_value(ev$value, ev$visible, envir)rlang::entrace(e), message = function (cnd) process_file(text, output) }{ TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) watcher$capture_plot_and_output()
if (on_message$capture) {50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$push(cnd) }
38: if (on_message$silence) {evaluate::evaluate(...)51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), invokeRestart("muffleMessage")39: output_dir = getwd(), ...)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
}}, warning = function (cnd) 52: keep_message = if (is.numeric(options$message)) TRUE else options$message, { stop_on_error = if (is.numeric(options$error)) options$error else { if (getOption("warn") >= 2 || getOption("warn") < 0) { if (options$error && options$include) vweave_rmarkdown(...) 0L return()
} else 2L53: }, output_handler = knit_handlers(options$render, options))
watcher$capture_plot_and_output()40: engine$weave(file, quiet = quiet, encoding = enc)in_dir(input_dir(), expr) if (on_warning$capture) {
54: 41: cnd <- sanitize_call(cnd)in_input_dir(evaluate(code, envir = env, new_device = FALSE, doTryCatch(return(expr), name, parentenv, handler) watcher$push(cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
55: }tryCatchOne(expr, names, parentenv, handlers[[1L]])
keep_message = if (is.numeric(options$message)) TRUE else options$message, 56: tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$error)) options$error else { if (on_warning$silence) {
if (options$error && options$include) invokeRestart("muffleWarning")57: 0L } else 2LtryCatch({}, error = function (cnd) engine$weave(file, quiet = quiet, encoding = enc){ }, output_handler = knit_handlers(options$render, options))) watcher$capture_plot_and_output() setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine) cnd <- sanitize_call(cnd) if (!have.makefile && vignette_is_tex(output)) { watcher$push(cnd)42: switch(on_error, continue = invokeRestart("eval_continue"), texi2pdf(file = output, clean = FALSE, quiet = quiet) stop = invokeRestart("eval_stop"), error = NULL)eng_r(options) output <- find_vignette_product(name, by = "texi2pdf", }) engine = engine)
}28: outputs <- c(outputs, output)eval(call)
43: }, error = function(e) {block_exec(params)29: thisOK <<- FALSE
fails <<- c(fails, file)eval(call)44: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", call_block(x)
file, conditionMessage(e)))
30: 45: process_group(group)})
with_handlers({46: 58: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { for (expr in tle$exprs) { if (progress && is.function(pb$interrupt)) pb$interrupt()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp0iJNcs/file92a62311a856.rds") error <<- format(e)
watcher$capture_plot_and_output()An irrecoverable exception occurred. R is aborting now ...
watcher$print_value(ev$value, ev$visible, envir) }) } TRUE
}, handlers)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 31: error = function(e) {doWithOneRestart(return(expr), restart) if (progress && is.function(pb$interrupt))
32: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(expr, restarts[[1L]]) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))33:
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {withRestartList(expr, restarts[-nr]) setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: 34: process_file(text, output)doWithOneRestart(return(expr), restart)
50: 35: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 36: output_dir = getwd(), ...)withRestartList(expr, restarts)
52:
vweave_rmarkdown(...)37:
withRestarts(with_handlers({53: engine$weave(file, quiet = quiet, encoding = enc) for (expr in tle$exprs) {
54: ev <- withVisible(eval(expr, envir))doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
55: watcher$print_value(ev$value, ev$visible, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
TRUE56: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)tryCatchList(expr, classes, parentenv, handlers)
38:
evaluate::evaluate(...)57:
tryCatch({39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, engine$weave(file, quiet = quiet, encoding = enc) keep_message = if (is.numeric(options$message)) TRUE else options$message, setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) stop_on_error = if (is.numeric(options$error)) options$error else { if (!have.makefile && vignette_is_tex(output)) { if (options$error && options$include) texi2pdf(file = output, clean = FALSE, quiet = quiet) 0L else 2L output <- find_vignette_product(name, by = "texi2pdf", }, output_handler = knit_handlers(options$render, options))
engine = engine) }40: in_dir(input_dir(), expr) outputs <- c(outputs, output)}, error = function(e) {
thisOK <<- FALSE41: fails <<- c(fails, file)in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) file, conditionMessage(e))) 0L}) else 2L
}, output_handler = knit_handlers(options$render, options)))
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 42: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp0iJNcs/file92a62311a856.rds")eng_r(options)
An irrecoverable exception occurred. R is aborting now ...
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)
Traceback:
setwd(startdir) 1: output <- find_vignette_product(name, by = "weave", engine = engine)RowCumsum(valid) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet) 2: output <- find_vignette_product(name, by = "texi2pdf", FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, engine = engine) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, } tieBreak = FALSE, verbose = verbose)
outputs <- c(outputs, output) 3: }, error = function(e) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, thisOK <<- FALSE tau = tau, theta = th, exclusionRadius = exclusionRadius, fails <<- c(fails, file) embedded = embedded, validLib = validLib, noTime = noTime, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", ignoreNan = ignoreNan, backend = backend)
file, conditionMessage(e))) 4: ComputeError(predictions$Observations, predictions$Predictions)})
5: 58: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", embedded = embedded, validLib = validLib, noTime = noTime, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp0iJNcs/file92a62311a856.rds") ignoreNan = ignoreNan, backend = backend)$predictions)
6: An irrecoverable exception occurred. R is aborting now ...
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$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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/Rtmp0iJNcs/file92a62311a856.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