Last updated on 2026-11-05 01:51:54 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 | 2.36 | 244.70 | 247.06 | 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 | 78.00 | 80.00 | 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
2026-11-05 05:50:20.091 R[45505:69859] 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({
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, for (expr in tle$exprs) { validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE
}, handlers)
3: 31: doWithOneRestart(return(expr), restart)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
32: withOneRestart(expr, restarts[[1L]]) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 33: ignoreNan = ignoreNan, backend = backend)withRestartList(expr, restarts[-nr])
34: 4: doWithOneRestart(return(expr), restart)ComputeError(predictions$Observations, predictions$Predictions)
5: 35: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 36: embedded = embedded, validLib = validLib, noTime = noTime, withRestartList(expr, restarts) ignoreNan = ignoreNan, backend = backend)$predictions)
6: 37: FUN(X[[i]], ...)withRestarts(with_handlers({
7: for (expr in tle$exprs) {lapply(X = S, FUN = FUN, ...)
ev <- withVisible(eval(expr, envir)) 8: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)doTryCatch(return(expr), name, parentenv, handler)
} 9: TRUEtryCatchOne(expr, names, parentenv, handlers[[1L]])}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
10: tryCatchList(expr, classes, parentenv, handlers)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) 0L11: else 2LtryCatch(expr, error = function(e) { }, 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$error else { call <- conditionCall(e) if (!is.null(call)) { if (options$error && options$include) if (identical(call[[1L]], quote(doTryCatch))) 0L call <- sys.call(-4L) else 2L dcall <- deparse(call, nlines = 1L) }, output_handler = knit_handlers(options$render, options))) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L42: sm <- strsplit(conditionMessage(e), "\n")[[1L]]eng_r(options) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
43: if (is.na(w)) block_exec(params) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) 44: prefix <- paste0(prefix, "\n ") } else prefix <- "Error : "call_block(x) msg <- paste0(prefix, conditionMessage(e), "\n")
45: process_group(group) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)46: .Internal(printDeferredWarnings())withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { invisible(structure(msg, class = "try-error", condition = e)) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 12: error <<- format(e)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: })
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 14: error = function(e) {FUN(X[[i]], ...)
if (progress && is.function(pb$interrupt)) 15: lapply(seq_len(cores), inner.do) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)16: }), list(rlang_trace_top_env = knit_global()))
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)48:
17: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), doTryCatch(return(expr), name, parentenv, handler) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt()18: if (is_R_CMD_build() || is_R_CMD_check()) tryCatchOne(expr, names, parentenv, handlers[[1L]]) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {19: setwd(wd)tryCatchList(expr, classes, parentenv, handlers) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 20: paste0("\n", rule(), error, "\n", rule()))tryCatch(parallel::mclapply(values, worker, mc.cores = cores, }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) mc.preschedule = TRUE), error = function(e) NULL)
49: 21: process_file(text, output)SweepApply(theta, worker, numProcess)
50:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)22:
unlist(SweepApply(theta, worker, numProcess))51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 23: output_dir = getwd(), ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
52: E = E, showPlot = TRUE)vweave_rmarkdown(...)
24:
53: eval(expr, envir)engine$weave(file, quiet = quiet, encoding = enc)
25: 54: eval(expr, envir)doTryCatch(return(expr), name, parentenv, handler)
26: 55: tryCatchOne(expr, names, parentenv, handlers[[1L]])withVisible(eval(expr, envir))
56: tryCatchList(expr, classes, parentenv, handlers)
27: 57: withCallingHandlers(code, error = function (e) tryCatch({rlang::entrace(e), message = function (cnd) engine$weave(file, quiet = quiet, encoding = enc){ setwd(startdir) watcher$capture_plot_and_output() output <- find_vignette_product(name, by = "weave", engine = engine) if (on_message$capture) { if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)
Traceback:
output <- find_vignette_product(name, by = "texi2pdf", watcher$push(cnd) 1: engine = engine)RowCumsum(valid) } }
outputs <- c(outputs, output) if (on_message$silence) { 2: invokeRestart("muffleMessage")}, error = function(e) { thisOK <<- FALSE } fails <<- c(fails, file)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, }, warning = function (cnd) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", validLib = validLib, libOverlap = idx$libOverlap, backend = backend, file, conditionMessage(e))) tieBreak = FALSE, verbose = verbose)}){
if (getOption("warn") >= 2 || getOption("warn") < 0) {58: 3: return()SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", } tau = tau, theta = th, exclusionRadius = exclusionRadius, watcher$capture_plot_and_output() embedded = embedded, validLib = validLib, noTime = noTime, skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpFGi8XU/file90a04ea9dca6.rds") ignoreNan = ignoreNan, backend = backend) if (on_warning$capture) {
cnd <- sanitize_call(cnd) 4:
ComputeError(predictions$Observations, predictions$Predictions) watcher$push(cnd)An irrecoverable exception occurred. R is aborting now ...
} 5: if (on_warning$silence) {SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, invokeRestart("muffleWarning") knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, } embedded = embedded, validLib = validLib, noTime = noTime, }, error = function (cnd) ignoreNan = ignoreNan, backend = backend)$predictions){
watcher$capture_plot_and_output() 6: cnd <- sanitize_call(cnd)FUN(X[[i]], ...)
watcher$push(cnd) 7: switch(on_error, continue = invokeRestart("eval_continue"), lapply(X = S, FUN = FUN, ...) stop = invokeRestart("eval_stop"), error = NULL)
8: })doTryCatch(return(expr), name, parentenv, handler)
28: eval(call) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])29:
eval(call)
10: 30: tryCatchList(expr, classes, parentenv, handlers)with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))11: watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { watcher$print_value(ev$value, ev$visible, envir) call <- conditionCall(e) } if (!is.null(call)) { TRUE if (identical(call[[1L]], quote(doTryCatch))) }, handlers) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")31: if (is.na(w)) doWithOneRestart(return(expr), restart) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) 32: prefix <- paste0(prefix, "\n ")withOneRestart(expr, restarts[[1L]]) }
else prefix <- "Error : "33: msg <- paste0(prefix, conditionMessage(e), "\n")withRestartList(expr, restarts[-nr])
.Internal(seterrmessage(msg[1L]))34: if (!silent && isTRUE(getOption("show.error.messages"))) {doWithOneRestart(return(expr), restart)
cat(msg, file = outFile)35: .Internal(printDeferredWarnings())withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) } invisible(structure(msg, class = "try-error", condition = e))
})36:
withRestartList(expr, restarts)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)37: withRestarts(with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))13: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
TRUE14: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)FUN(X[[i]], ...)
38: 15: evaluate::evaluate(...)
lapply(seq_len(cores), inner.do)
39: 16: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) keep_message = if (is.numeric(options$message)) TRUE else options$message,
17: stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0LdoTryCatch(return(expr), name, parentenv, handler) else 2L }, output_handler = knit_handlers(options$render, options))
18: 40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
in_dir(input_dir(), expr)19: tryCatchList(expr, classes, parentenv, handlers)
20: 41: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, in_input_dir(evaluate(code, envir = env, new_device = FALSE, mc.preschedule = TRUE), error = function(e) NULL) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 21: stop_on_error = if (is.numeric(options$error)) options$error else {SweepApply(theta, worker, numProcess) if (options$error && options$include) 0L
else 2L22: }, output_handler = knit_handlers(options$render, options)))unlist(SweepApply(theta, worker, numProcess))
42: 23: eng_r(options)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
43: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", block_exec(params) E = E, showPlot = TRUE)
44: 24: call_block(x)
eval(expr, envir)45:
process_group(group)25:
46: eval(expr, envir)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {26: if (progress && is.function(pb$interrupt)) withVisible(eval(expr, envir)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)27: })withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 47: {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() error = function(e) { if (progress && is.function(pb$interrupt)) if (on_message$capture) { pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) if (on_message$silence) { }), list(rlang_trace_top_env = knit_global())) invokeRestart("muffleMessage")
48: }xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, warning = function (cnd) error = function(e) {{ if (progress && is.function(pb$interrupt)) if (getOption("warn") >= 2 || getOption("warn") < 0) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) return() error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { } setwd(wd) watcher$capture_plot_and_output() write_utf8(res, output %n% stdout()) if (on_warning$capture) { paste0("\nQuitting from ", loc, if (!is.null(error)) cnd <- sanitize_call(cnd) watcher$push(cnd) } paste0("\n", rule(), error, "\n", rule())) if (on_warning$silence) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) invokeRestart("muffleWarning") }
}, error = function (cnd) 49: {process_file(text, output) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)50: watcher$push(cnd)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }) output_dir = getwd(), ...)
28: 52: eval(call)vweave_rmarkdown(...)
29: 53: eval(call)engine$weave(file, quiet = quiet, encoding = enc)
54: 30: doTryCatch(return(expr), name, parentenv, handler)with_handlers({
for (expr in tle$exprs) {55: ev <- withVisible(eval(expr, envir))tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()
56: watcher$print_value(ev$value, ev$visible, envir)tryCatchList(expr, classes, parentenv, handlers) }
TRUE57: }, handlers)tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)31: doWithOneRestart(return(expr), restart) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 32: engine = engine)withOneRestart(expr, restarts[[1L]]) } outputs <- c(outputs, output)}, error = function(e) {
thisOK <<- FALSE33: fails <<- c(fails, file)withRestartList(expr, restarts[-nr]) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpFGi8XU/file90a04ea9dca6.rds")
An irrecoverable exception occurred. R is aborting now ...
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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)))
Traceback:
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$interrupt)) 1: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tieBreak = FALSE, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, error <<- format(e) ignoreNan = ignoreNan, backend = backend) })
47: 4: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$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$interrupt()ComputeError(predictions$Observations, predictions$Predictions) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { 5: setwd(wd) write_utf8(res, output %n% stdout())SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$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]])
paste0("\nQuitting from ", loc, if (!is.null(error)) 10: paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)tryCatchList(expr, classes, parentenv, handlers)
11: 49: tryCatch(expr, error = function(e) {process_file(text, output) call <- conditionCall(e)
50: if (!is.null(call)) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)51: dcall <- deparse(call, nlines = 1L)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: prefix <- paste("Error in", dcall, ": ")vweave_rmarkdown(...)
53: 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) engine$weave(file, quiet = quiet, encoding = enc) prefix <- paste0(prefix, "\n ")
}54: doTryCatch(return(expr), name, parentenv, handler) else prefix <- "Error : "
55: msg <- paste0(prefix, conditionMessage(e), "\n")tryCatchOne(expr, names, parentenv, handlers[[1L]])
.Internal(seterrmessage(msg[1L]))56: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatchList(expr, classes, parentenv, handlers) cat(msg, file = outFile)
.Internal(printDeferredWarnings())57: tryCatch({ } invisible(structure(msg, class = "try-error", condition = e)) engine$weave(file, quiet = quiet, encoding = enc)}) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)12: if (!have.makefile && vignette_is_tex(output)) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 13: engine = engine)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
14: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file)FUN(X[[i]], ...) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))15: lapply(seq_len(cores), inner.do)})
16: 58: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 17: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpFGi8XU/file90a04ea9dca6.rds")doTryCatch(return(expr), name, parentenv, handler)
An irrecoverable exception occurred. R is aborting now ...
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/RtmpFGi8XU/file90a04ea9dca6.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