Last updated on 2026-10-17 02:52:52 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 | 2.47 | 224.20 | 226.67 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 178.80 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.02 | 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 | 3.18 | 212.69 | 215.87 | 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 | 2.00 | 35.00 | 37.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 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
2026-10-17 08:30:26.675 R[50424:76827] 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'
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)
Traceback:
1: 17: RowCumsum(valid)doTryCatch(return(expr), name, parentenv, handler)
2: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 19: tieBreak = FALSE, verbose = verbose)tryCatchList(expr, classes, parentenv, handlers)
3: 20: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tau = tau, theta = th, exclusionRadius = exclusionRadius, mc.preschedule = TRUE), error = function(e) NULL) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)21:
SweepApply(theta, worker, numProcess) 4:
ComputeError(predictions$Observations, predictions$Predictions)22:
unlist(SweepApply(theta, worker, numProcess)) 5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 23: embedded = embedded, validLib = validLib, noTime = noTime, PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", ignoreNan = ignoreNan, backend = backend)$predictions) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
6: 24: FUN(X[[i]], ...)eval(expr, envir)
7: 25: lapply(X = S, FUN = FUN, ...)eval(expr, envir)
26: 8: withVisible(eval(expr, envir))doTryCatch(return(expr), name, parentenv, handler)
27: 9: withCallingHandlers(code, error = function (e) tryCatchOne(expr, names, parentenv, handlers[[1L]])rlang::entrace(e), message = function (cnd)
{10: watcher$capture_plot_and_output()tryCatchList(expr, classes, parentenv, handlers)
if (on_message$capture) {11: watcher$push(cnd)tryCatch(expr, error = function(e) { } call <- conditionCall(e) if (on_message$silence) { if (!is.null(call)) { invokeRestart("muffleMessage") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L)}, warning = function (cnd) dcall <- deparse(call, nlines = 1L){ if (getOption("warn") >= 2 || getOption("warn") < 0) { prefix <- paste("Error in", dcall, ": ") return() LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]] watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (on_warning$capture) { if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], cnd <- sanitize_call(cnd) type = "b") watcher$push(cnd) if (w > LONG) } prefix <- paste0(prefix, "\n ") if (on_warning$silence) { } invokeRestart("muffleWarning") else prefix <- "Error : " } msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))}, error = function (cnd) if (!silent && isTRUE(getOption("show.error.messages"))) {{ watcher$capture_plot_and_output() cat(msg, file = outFile) cnd <- sanitize_call(cnd) .Internal(printDeferredWarnings()) watcher$push(cnd) } switch(on_error, continue = invokeRestart("eval_continue"), invisible(structure(msg, class = "try-error", condition = e)) stop = invokeRestart("eval_stop"), error = NULL)})
12: })try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
28: 13: eval(call)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: 14: eval(call)FUN(X[[i]], ...)
15: 30: with_handlers({lapply(seq_len(cores), inner.do)
for (expr in tle$exprs) {16: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$print_value(ev$value, ev$visible, envir)
}17: TRUEdoTryCatch(return(expr), name, parentenv, handler)}, handlers)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])31:
19: doWithOneRestart(return(expr), restart)tryCatchList(expr, classes, parentenv, handlers)
32: 20: withOneRestart(expr, restarts[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)33:
withRestartList(expr, restarts[-nr])21:
SweepApply(theta, worker, numProcess)34:
doWithOneRestart(return(expr), restart)22: unlist(SweepApply(theta, worker, numProcess))
35: 23: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
E = E, showPlot = TRUE)36:
24: withRestartList(expr, restarts)eval(expr, envir)
37: 25: withRestarts(with_handlers({eval(expr, envir) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))26: watcher$capture_plot_and_output()withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir)
*** caught segfault ***
}27: address 0x110, cause 'invalid permissions'
TRUE
Traceback:
withCallingHandlers(code, error = function (e) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)rlang::entrace(e), message = function (cnd) 1:
{RowCumsum(valid) watcher$capture_plot_and_output()38:
evaluate::evaluate(...) 2: if (on_message$capture) {
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, watcher$push(cnd)39: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tieBreak = FALSE, verbose = verbose) if (on_message$silence) { keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { invokeRestart("muffleMessage") if (options$error && options$include) } 3: }, warning = function (cnd) 0L{ else 2L if (getOption("warn") >= 2 || getOption("warn") < 0) { }, output_handler = knit_handlers(options$render, options))SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, return()
tau = tau, theta = th, exclusionRadius = exclusionRadius, }40: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)in_dir(input_dir(), expr) watcher$capture_plot_and_output()
if (on_warning$capture) {41: cnd <- sanitize_call(cnd) 4: watcher$push(cnd)ComputeError(predictions$Observations, predictions$Predictions)in_input_dir(evaluate(code, envir = env, new_device = FALSE, }
if (on_warning$silence) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleWarning") 5: keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, }, error = function (cnd) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (options$error && options$include) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions) 0L{
else 2L 6: watcher$capture_plot_and_output()FUN(X[[i]], ...) cnd <- sanitize_call(cnd) }, output_handler = knit_handlers(options$render, options)))
watcher$push(cnd) 7:
lapply(X = S, FUN = FUN, ...)
42: 8: switch(on_error, continue = invokeRestart("eval_continue"), eng_r(options)doTryCatch(return(expr), name, parentenv, handler) stop = invokeRestart("eval_stop"), error = NULL)
})
43:
block_exec(params) 9:
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])28: call_block(x)
eval(call)10:
tryCatchList(expr, classes, parentenv, handlers)
45: 11: 29: process_group(group)tryCatch(expr, error = function(e) { call <- conditionCall(e)eval(call)
if (!is.null(call)) {
46: if (identical(call[[1L]], quote(doTryCatch))) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 30: error = function(e) {with_handlers({ if (progress && is.function(pb$interrupt)) call <- sys.call(-4L) for (expr in tle$exprs) { dcall <- deparse(call, nlines = 1L) pb$interrupt() prefix <- paste("Error in", dcall, ": ") ev <- withVisible(eval(expr, envir)) LONG <- 75L if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") error <<- format(e) watcher$print_value(ev$value, ev$visible, envir) }) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], TRUE type = "b")
if (w > LONG) }, handlers) prefix <- paste0(prefix, "\n ")47:
}with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 31: else prefix <- "Error : "doWithOneRestart(return(expr), restart) msg <- paste0(prefix, conditionMessage(e), "\n") error = function(e) { .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) if (progress && is.function(pb$interrupt))
pb$interrupt() .Internal(printDeferredWarnings()) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e)32: invisible(structure(msg, class = "try-error", condition = e))withOneRestart(expr, restarts[[1L]])
}), list(rlang_trace_top_env = knit_global()))33: })withRestartList(expr, restarts[-nr])
48: 12:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), try(lapply(X = S, FUN = FUN, ...), silent = TRUE)34: error = function(e) {
if (progress && is.function(pb$interrupt)) 13: doWithOneRestart(return(expr), restart)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
pb$interrupt()35: if (is_R_CMD_build() || is_R_CMD_check()) 14: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])FUN(X[[i]], ...) }), list(rlang_trace_top_env = knit_global())), function(loc) {
15: 36: setwd(wd)lapply(seq_len(cores), inner.do)withRestartList(expr, restarts) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 16: paste0("\n", rule(), error, "\n", rule()))parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)37:
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)withRestarts(with_handlers({17: for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))doTryCatch(return(expr), name, parentenv, handler)49: watcher$capture_plot_and_output()
process_file(text, output) watcher$print_value(ev$value, ev$visible, envir)
18: }50: TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]])}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
19: 38: tryCatchList(expr, classes, parentenv, handlers)51:
evaluate::evaluate(...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 20: output_dir = getwd(), ...)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)
52: 21: 39: SweepApply(theta, worker, numProcess)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, vweave_rmarkdown(...)22: stop_on_error = if (is.numeric(options$error)) options$error else {unlist(SweepApply(theta, worker, numProcess))
53: if (options$error && options$include) 23: engine$weave(file, quiet = quiet, encoding = enc)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 0L target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
else 2L54: E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler)
}, output_handler = knit_handlers(options$render, options))24: 55:
eval(expr, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]])40:
in_dir(input_dir(), expr)
25: 56: tryCatchList(expr, classes, parentenv, handlers)
eval(expr, envir)41:
57: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tryCatch({ keep_message = if (is.numeric(options$message)) TRUE else options$message, 26: stop_on_error = if (is.numeric(options$error)) options$error else { engine$weave(file, quiet = quiet, encoding = enc)withVisible(eval(expr, envir)) setwd(startdir) if (options$error && options$include) output <- find_vignette_product(name, by = "weave", engine = engine)
0L if (!have.makefile && vignette_is_tex(output)) {27: texi2pdf(file = output, clean = FALSE, quiet = quiet)withCallingHandlers(code, error = function (e) output <- find_vignette_product(name, by = "texi2pdf", else 2Lrlang::entrace(e), message = function (cnd) }, output_handler = knit_handlers(options$render, options))) engine = engine){
} watcher$capture_plot_and_output() outputs <- c(outputs, output) if (on_message$capture) { watcher$push(cnd)}, error = function(e) {42: thisOK <<- FALSEeng_r(options) fails <<- c(fails, file) } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (on_message$silence) {
invokeRestart("muffleMessage") file, conditionMessage(e))) }43: })}, warning = function (cnd)
{block_exec(params) if (getOption("warn") >= 2 || getOption("warn") < 0) {58:
return()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 44: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5SZqXh/file9aba5bb05a10.rds") }
watcher$capture_plot_and_output()call_block(x) if (on_warning$capture) {An irrecoverable exception occurred. R is aborting now ...
cnd <- sanitize_call(cnd)45: watcher$push(cnd) }process_group(group) if (on_warning$silence) { invokeRestart("muffleWarning")
}46: }, error = function (cnd) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) error <<- format(e)}) })
28:
eval(call)
47: 29: eval(call)
30: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), with_handlers({ for (expr in tle$exprs) { error = function(e) { ev <- withVisible(eval(expr, envir)) if (progress && is.function(pb$interrupt)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) TRUE error <<- format(e)}, handlers)
}), list(rlang_trace_top_env = knit_global()))31: doWithOneRestart(return(expr), restart)
32:
withOneRestart(expr, restarts[[1L]])
33: 48: withRestartList(expr, restarts[-nr])xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {34: if (progress && is.function(pb$interrupt)) doWithOneRestart(return(expr), restart) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 35: error <<- format(e)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
write_utf8(res, output %n% stdout())36: paste0("\nQuitting from ", loc, if (!is.null(error)) withRestartList(expr, restarts) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)37:
withRestarts(with_handlers({49: for (expr in tle$exprs) {process_file(text, output) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()50: watcher$print_value(ev$value, ev$visible, envir)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }
51: TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)38:
evaluate::evaluate(...)52:
vweave_rmarkdown(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 53: keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 54: 0LdoTryCatch(return(expr), name, parentenv, handler) else 2L
}, output_handler = knit_handlers(options$render, options))55:
tryCatchOne(expr, names, parentenv, handlers[[1L]])40:
in_dir(input_dir(), expr)56: tryCatchList(expr, classes, parentenv, handlers)
41: 57: in_input_dir(evaluate(code, envir = env, new_device = FALSE, tryCatch({ keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc) stop_on_error = if (is.numeric(options$error)) options$error else { setwd(startdir) if (options$error && options$include) 0L output <- find_vignette_product(name, by = "weave", engine = engine) else 2L if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) }, output_handler = knit_handlers(options$render, options)))
output <- find_vignette_product(name, by = "texi2pdf", 42: engine = engine)eng_r(options) }
outputs <- c(outputs, output)43: }, error = function(e) {block_exec(params) thisOK <<- FALSE
fails <<- c(fails, file)44: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", call_block(x)
file, conditionMessage(e)))45: })
process_group(group)58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 46: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5SZqXh/file9aba5bb05a10.rds")withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {An irrecoverable exception occurred. R is aborting now ...
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())
Traceback:
1: error <<- format(e)RowCumsum(valid) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)
write_utf8(res, output %n% stdout()) 2: paste0("\nQuitting from ", loc, if (!is.null(error)) FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, paste0("\n", rule(), error, "\n", rule())) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) tieBreak = FALSE, verbose = verbose)
49: 3: process_file(text, output)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, 50: embedded = embedded, validLib = validLib, noTime = noTime, knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) ignoreNan = ignoreNan, backend = backend)
51: 4: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ComputeError(predictions$Observations, predictions$Predictions) output_dir = getwd(), ...)
5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 52: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, vweave_rmarkdown(...) embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
53: 6: engine$weave(file, quiet = quiet, encoding = enc)FUN(X[[i]], ...)
54: 7: doTryCatch(return(expr), name, parentenv, handler)lapply(X = S, FUN = FUN, ...)
55: 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchList(expr, classes, parentenv, handlers) 9:
57: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)10: if (!have.makefile && vignette_is_tex(output)) {tryCatchList(expr, classes, parentenv, handlers) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }11: outputs <- c(outputs, output)tryCatch(expr, error = function(e) {}, error = function(e) { thisOK <<- FALSE call <- conditionCall(e) fails <<- c(fails, file) if (!is.null(call)) { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)}) dcall <- deparse(call, nlines = 1L)
58: prefix <- paste("Error in", dcall, ": ")tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5SZqXh/file9aba5bb05a10.rds") LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]An irrecoverable exception occurred. R is aborting now ...
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/Rtmp5SZqXh/file9aba5bb05a10.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