Last updated on 2026-10-16 15:51:35 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.38 | 227.64 | 231.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.64 | 244.80 | 247.44 | 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 | 6.00 | 141.00 | 147.00 | 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 | 5.00 | 137.00 | 142.00 | 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 01:54:51.258 R[46004:71364] 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)
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:
Traceback:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 1: error = function(e) {RowCumsum(valid) if (progress && is.function(pb$interrupt))
Traceback:
pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 1: 2: error <<- format(e)RowCumsum(valid)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, }), list(rlang_trace_top_env = knit_global())) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose) 2: 48: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 3: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tieBreak = FALSE, verbose = verbose)SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, error = function(e) {
if (progress && is.function(pb$interrupt)) tau = tau, theta = th, exclusionRadius = exclusionRadius, pb$interrupt() embedded = embedded, validLib = validLib, noTime = noTime, if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) 3: ignoreNan = ignoreNan, backend = backend) }), list(rlang_trace_top_env = knit_global())), function(loc) {SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
tau = tau, theta = th, exclusionRadius = exclusionRadius, setwd(wd) embedded = embedded, validLib = validLib, noTime = noTime, 4: ignoreNan = ignoreNan, backend = backend) write_utf8(res, output %n% stdout())
ComputeError(predictions$Observations, predictions$Predictions) paste0("\nQuitting from ", loc, if (!is.null(error)) 4:
paste0("\n", rule(), error, "\n", rule()))ComputeError(predictions$Observations, predictions$Predictions)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 49: 5: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, process_file(text, output) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 50:
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 6: embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)FUN(X[[i]], ...)
6: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)FUN(X[[i]], ...)
*** caught segfault ***
51:
address 0x110, cause 'invalid permissions'
7: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), lapply(X = S, FUN = FUN, ...) output_dir = getwd(), ...) 7:
lapply(X = S, FUN = FUN, ...)
8: 8: doTryCatch(return(expr), name, parentenv, handler)
doTryCatch(return(expr), name, parentenv, handler)52:
9: vweave_rmarkdown(...) 9:
53: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])engine$weave(file, quiet = quiet, encoding = enc)
10: tryCatchList(expr, classes, parentenv, handlers)
10: 11: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) {54: call <- conditionCall(e)doTryCatch(return(expr), name, parentenv, handler) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 55: call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L56: 11: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")tryCatchList(expr, classes, parentenv, handlers) if (is.na(w))
call <- conditionCall(e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 57: type = "b")tryCatch({ if (!is.null(call)) { if (w > LONG) prefix <- paste0(prefix, "\n ") if (identical(call[[1L]], quote(doTryCatch))) } engine$weave(file, quiet = quiet, encoding = enc) else prefix <- "Error : " setwd(startdir) call <- sys.call(-4L) msg <- paste0(prefix, conditionMessage(e), "\n") output <- find_vignette_product(name, by = "weave", engine = engine) dcall <- deparse(call, nlines = 1L) .Internal(seterrmessage(msg[1L])) if (!have.makefile && vignette_is_tex(output)) { prefix <- paste("Error in", dcall, ": ") if (!silent && isTRUE(getOption("show.error.messages"))) { texi2pdf(file = output, clean = FALSE, quiet = quiet) LONG <- 75L cat(msg, file = outFile) output <- find_vignette_product(name, by = "texi2pdf", sm <- strsplit(conditionMessage(e), "\n")[[1L]] .Internal(printDeferredWarnings()) engine = engine) } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") } invisible(structure(msg, class = "try-error", condition = e)) if (is.na(w)) outputs <- c(outputs, output)}) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], }, error = function(e) { type = "b")
if (w > LONG) thisOK <<- FALSE prefix <- paste0(prefix, "\n ")12: } else prefix <- "Error : " fails <<- c(fails, file)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
msg <- paste0(prefix, conditionMessage(e), "\n")13: file, conditionMessage(e))) .Internal(seterrmessage(msg[1L]))sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))})
if (!silent && isTRUE(getOption("show.error.messages"))) {
14: 58: FUN(X[[i]], ...) cat(msg, file = outFile)
15: .Internal(printDeferredWarnings())lapply(seq_len(cores), inner.do)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM",
skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3jwEFR/file97022febcdf8.rds") }
invisible(structure(msg, class = "try-error", condition = e))16: })An irrecoverable exception occurred. R is aborting now ...
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
17: 13: doTryCatch(return(expr), name, parentenv, handler)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])14:
FUN(X[[i]], ...)19:
tryCatchList(expr, classes, parentenv, handlers)15:
lapply(seq_len(cores), inner.do)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 16: mc.preschedule = TRUE), error = function(e) NULL)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 21: doTryCatch(return(expr), name, parentenv, handler)SweepApply(theta, worker, numProcess)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: unlist(SweepApply(theta, worker, numProcess))19:
tryCatchList(expr, classes, parentenv, handlers)
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", mc.preschedule = TRUE), error = function(e) NULL) E = E, showPlot = TRUE)
21: SweepApply(theta, worker, numProcess)24:
eval(expr, envir)22:
unlist(SweepApply(theta, worker, numProcess))
25: 23: eval(expr, envir)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 26: withVisible(eval(expr, envir)) E = E, showPlot = TRUE)
27: withCallingHandlers(code, error = function (e) 24: eval(expr, envir)rlang::entrace(e), message = function (cnd)
{25: watcher$capture_plot_and_output()eval(expr, envir) if (on_message$capture) {
watcher$push(cnd)26: }withVisible(eval(expr, envir)) if (on_message$silence) {
27: invokeRestart("muffleMessage")withCallingHandlers(code, error = function (e) }rlang::entrace(e), message = function (cnd) {}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() watcher$capture_plot_and_output() if (on_message$capture) { } watcher$push(cnd) watcher$capture_plot_and_output() if (on_warning$capture) { } cnd <- sanitize_call(cnd) if (on_message$silence) { watcher$push(cnd) invokeRestart("muffleMessage") } } if (on_warning$silence) {}, warning = function (cnd) invokeRestart("muffleWarning"){ }}, error = function (cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) {{ watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) return() watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL)})
watcher$capture_plot_and_output()28: eval(call)
if (on_warning$capture) {29: cnd <- sanitize_call(cnd)eval(call) watcher$push(cnd)
}30: if (on_warning$silence) {with_handlers({ invokeRestart("muffleWarning") for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir))}, error = function (cnd) watcher$capture_plot_and_output(){ watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd) watcher$push(cnd) TRUE switch(on_error, continue = invokeRestart("eval_continue"), }, handlers) stop = invokeRestart("eval_stop"), error = NULL)
})31:
doWithOneRestart(return(expr), restart)28:
eval(call)32:
29: withOneRestart(expr, restarts[[1L]])eval(call)
33: 30: withRestartList(expr, restarts[-nr])with_handlers({
for (expr in tle$exprs) {34: ev <- withVisible(eval(expr, envir))doWithOneRestart(return(expr), restart) watcher$capture_plot_and_output()
35: watcher$print_value(ev$value, ev$visible, envir)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) }
TRUE36: }, handlers)withRestartList(expr, restarts)
31: 37: withRestarts(with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {
32: ev <- withVisible(eval(expr, envir))withOneRestart(expr, restarts[[1L]]) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)33: } TRUEwithRestartList(expr, restarts[-nr])}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
34: doWithOneRestart(return(expr), restart)38:
evaluate::evaluate(...)
35: 39: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 36: stop_on_error = if (is.numeric(options$error)) options$error else {withRestartList(expr, restarts) if (options$error && options$include) 0L
else 2L }, output_handler = knit_handlers(options$render, options))37:
withRestarts(with_handlers({40: for (expr in tle$exprs) {in_dir(input_dir(), expr)
ev <- withVisible(eval(expr, envir))41: watcher$capture_plot_and_output()in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$print_value(ev$value, ev$visible, envir) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } keep_message = if (is.numeric(options$message)) TRUE else options$message, TRUE stop_on_error = if (is.numeric(options$error)) options$error else {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (options$error && options$include)
0L38: else 2Levaluate::evaluate(...) }, output_handler = knit_handlers(options$render, options)))
39: 42: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, eng_r(options) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {43: if (options$error && options$include) block_exec(params) 0L
else 2L44: }, output_handler = knit_handlers(options$render, options))call_block(x)
40: 45: in_dir(input_dir(), expr)process_group(group)
41: 46: in_input_dir(evaluate(code, envir = env, new_device = FALSE, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, if (progress && is.function(pb$interrupt)) stop_on_error = if (is.numeric(options$error)) options$error else { pb$interrupt() if (options$error && options$include) if (is_R_CMD_build() || is_R_CMD_check()) 0L error <<- format(e) else 2L }) }, output_handler = knit_handlers(options$render, options)))
47: 42: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eng_r(options) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt()43: if (is_R_CMD_build() || is_R_CMD_check()) block_exec(params) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))44:
call_block(x)48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: error = function(e) {process_group(group) if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error <<- format(e) error = function(e) { if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt() setwd(wd) if (is_R_CMD_build() || is_R_CMD_check()) write_utf8(res, output %n% stdout()) error <<- format(e) paste0("\nQuitting from ", loc, if (!is.null(error)) }) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 49: error = function(e) {process_file(text, output) if (progress && is.function(pb$interrupt))
pb$interrupt()50: if (is_R_CMD_build() || is_R_CMD_check()) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))51:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 48: output_dir = getwd(), ...)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {52: vweave_rmarkdown(...) if (progress && is.function(pb$interrupt))
53: pb$interrupt()engine$weave(file, quiet = quiet, encoding = enc) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)54: }), list(rlang_trace_top_env = knit_global())), function(loc) {doTryCatch(return(expr), name, parentenv, handler) setwd(wd)
write_utf8(res, output %n% stdout())55: paste0("\nQuitting from ", loc, if (!is.null(error)) tryCatchOne(expr, names, parentenv, handlers[[1L]]) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)56:
tryCatchList(expr, classes, parentenv, handlers)49:
process_file(text, output)57:
tryCatch({50: engine$weave(file, quiet = quiet, encoding = enc)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)51: if (!have.makefile && vignette_is_tex(output)) {rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), texi2pdf(file = output, clean = FALSE, quiet = quiet) output_dir = getwd(), ...) output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)52: } outputs <- c(outputs, output)vweave_rmarkdown(...)}, error = function(e) {
thisOK <<- FALSE53: fails <<- c(fails, file)engine$weave(file, quiet = quiet, encoding = enc) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))54: })
doTryCatch(return(expr), name, parentenv, handler)58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 55: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3jwEFR/file97022febcdf8.rds")tryCatchOne(expr, names, parentenv, handlers[[1L]])
An irrecoverable exception occurred. R is aborting now ...
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$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)
Traceback:
output <- find_vignette_product(name, by = "texi2pdf", 1: engine = engine)RowCumsum(valid)
2: }FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, outputs <- c(outputs, output) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, }, error = function(e) { tieBreak = FALSE, verbose = verbose) thisOK <<- FALSE
fails <<- c(fails, file) 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", tau = tau, theta = th, exclusionRadius = exclusionRadius, file, conditionMessage(e))) embedded = embedded, validLib = validLib, noTime = noTime, })
ignoreNan = ignoreNan, backend = backend)58:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", 4: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3jwEFR/file97022febcdf8.rds")
ComputeError(predictions$Observations, predictions$Predictions)An irrecoverable exception occurred. R is aborting now ...
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
28: eval(call)
29: eval(call)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ for (expr in tle$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/Rtmp3jwEFR/file97022febcdf8.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