Last updated on 2026-10-08 23:52:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 2.91 | 225.24 | 228.15 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.42 | 229.06 | 231.48 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 179.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.79 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.60 | 213.69 | 217.29 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 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 | 129.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 6.00 | 157.00 | 163.00 | 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
2026-10-09 05:32:01.734 R[42237:64652] XType: Using static font registry.
*** 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$capture_plot_and_output()
*** caught segfault ***
address 0x110, cause 'invalid permissions'
if (on_warning$capture) { cnd <- sanitize_call(cnd)
*** caught segfault ***
watcher$push(cnd)address 0x110, cause 'invalid permissions'
} if (on_warning$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)
Traceback:
43: 1: block_exec(params)RowCumsum(valid)
44:
call_block(x) 2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 45: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, process_group(group) tieBreak = FALSE, verbose = verbose)
46: 3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tau = tau, theta = th, exclusionRadius = exclusionRadius, error = function(e) { if (progress && is.function(pb$interrupt)) embedded = embedded, validLib = validLib, noTime = noTime, pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) ignoreNan = ignoreNan, backend = backend) error <<- format(e) })
4: 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ComputeError(predictions$Observations, predictions$Predictions) error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 5: error <<- format(e)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, }), list(rlang_trace_top_env = knit_global())) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, 48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ignoreNan = ignoreNan, backend = backend)$predictions) error = function(e) {
6: if (progress && is.function(pb$interrupt)) pb$interrupt()FUN(X[[i]], ...) if (is_R_CMD_build() || is_R_CMD_check())
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
error <<- format(e) 9: }), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatchOne(expr, names, parentenv, handlers[[1L]]) setwd(wd)
write_utf8(res, output %n% stdout())10: paste0("\nQuitting from ", loc, if (!is.null(error)) tryCatchList(expr, classes, parentenv, handlers) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)11:
tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) {49: process_file(text, output) if (identical(call[[1L]], quote(doTryCatch)))
50: call <- sys.call(-4L)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")51: LONG <- 75Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), sm <- strsplit(conditionMessage(e), "\n")[[1L]] output_dir = getwd(), ...) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 52: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], vweave_rmarkdown(...) type = "b")
if (w > LONG) prefix <- paste0(prefix, "\n ")53: }engine$weave(file, quiet = quiet, encoding = enc) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")54: .Internal(seterrmessage(msg[1L]))doTryCatch(return(expr), name, parentenv, handler) if (!silent && isTRUE(getOption("show.error.messages"))) {
55: cat(msg, file = outFile)tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(printDeferredWarnings())
}56: invisible(structure(msg, class = "try-error", condition = e))tryCatchList(expr, classes, parentenv, handlers)})
57: 12: tryCatch({try(lapply(X = S, FUN = FUN, ...), silent = TRUE) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)13: output <- find_vignette_product(name, by = "weave", engine = engine)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)14: output <- find_vignette_product(name, by = "texi2pdf", engine = engine)FUN(X[[i]], ...) }
outputs <- c(outputs, output)15: }, error = function(e) {lapply(seq_len(cores), inner.do) thisOK <<- FALSE
fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))16: })
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)58:
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/RtmpbWT6Xp/file8bb456e831d3.rds")doTryCatch(return(expr), name, parentenv, handler)
18: An irrecoverable exception occurred. R is aborting now ...
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) {
Traceback:
ev <- withVisible(eval(expr, envir)) 1:
Traceback:
watcher$capture_plot_and_output()RowCumsum(valid) watcher$print_value(ev$value, ev$visible, envir) 1: RowCumsum(valid) }
TRUE 2: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 38: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, evaluate::evaluate(...) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose) tieBreak = FALSE, verbose = verbose)39:
3:
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, tau = tau, theta = th, exclusionRadius = exclusionRadius, SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, keep_message = if (is.numeric(options$message)) TRUE else options$message, embedded = embedded, validLib = validLib, noTime = noTime, tau = tau, theta = th, exclusionRadius = exclusionRadius, stop_on_error = if (is.numeric(options$error)) options$error else { ignoreNan = ignoreNan, backend = backend) if (options$error && options$include)
embedded = embedded, validLib = validLib, noTime = noTime, 0L 4: ignoreNan = ignoreNan, backend = backend)
ComputeError(predictions$Observations, predictions$Predictions) else 2L 4:
}, output_handler = knit_handlers(options$render, options))ComputeError(predictions$Observations, predictions$Predictions) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 40: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, in_dir(input_dir(), expr)
embedded = embedded, validLib = validLib, noTime = noTime, 5: ignoreNan = ignoreNan, backend = backend)$predictions)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
41: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 6: in_input_dir(evaluate(code, envir = env, new_device = FALSE, FUN(X[[i]], ...) embedded = embedded, validLib = validLib, noTime = noTime, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, ignoreNan = ignoreNan, backend = backend)$predictions)
keep_message = if (is.numeric(options$message)) TRUE else options$message,
6: 7: FUN(X[[i]], ...)lapply(X = S, FUN = FUN, ...)
7: 8: lapply(X = S, FUN = FUN, ...)
stop_on_error = if (is.numeric(options$error)) options$error else { 8: doTryCatch(return(expr), name, parentenv, handler)
if (options$error && options$include) 9: doTryCatch(return(expr), name, parentenv, handler)tryCatchOne(expr, names, parentenv, handlers[[1L]]) 0L
else 2L
9: }, output_handler = knit_handlers(options$render, options)))10: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
42:
eng_r(options)
11: 43: 10: block_exec(params)tryCatch(expr, error = function(e) {
tryCatchList(expr, classes, parentenv, handlers)44: call <- conditionCall(e)
if (!is.null(call)) {call_block(x) if (identical(call[[1L]], quote(doTryCatch))) 11:
45: tryCatch(expr, error = function(e) { call <- conditionCall(e)process_group(group) if (!is.null(call)) { call <- sys.call(-4L) if (identical(call[[1L]], quote(doTryCatch))) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L)46: dcall <- deparse(call, nlines = 1L) LONG <- 75LwithCallingHandlers(if (tangle) process_tangle(group) else process_group(group), sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") error = function(e) { w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (progress && is.function(pb$interrupt)) LONG <- 75L pb$interrupt() if (is.na(w)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (is_R_CMD_build() || is_R_CMD_check()) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) error <<- format(e) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") type = "b") if (w > LONG) if (w > LONG) }) prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : "47: msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste0(prefix, "\n ") .Internal(seterrmessage(msg[1L]))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { if (!silent && isTRUE(getOption("show.error.messages"))) { else prefix <- "Error : " if (progress && is.function(pb$interrupt)) msg <- paste0(prefix, conditionMessage(e), "\n") pb$interrupt() cat(msg, file = outFile) .Internal(seterrmessage(msg[1L])) if (is_R_CMD_build() || is_R_CMD_check()) if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(printDeferredWarnings()) cat(msg, file = outFile) error <<- format(e) } }), list(rlang_trace_top_env = knit_global())) invisible(structure(msg, class = "try-error", condition = e))
}) .Internal(printDeferredWarnings())48: }
invisible(structure(msg, class = "try-error", condition = e))12: })xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
error = function(e) {
12: if (progress && is.function(pb$interrupt)) 13: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) pb$interrupt()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)13: 14: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
FUN(X[[i]], ...)14:
setwd(wd)15: FUN(X[[i]], ...)lapply(seq_len(cores), inner.do)
write_utf8(res, output %n% stdout())16:
paste0("\nQuitting from ", loc, if (!is.null(error)) parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) paste0("\n", rule(), error, "\n", rule()))
15: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)17: doTryCatch(return(expr), name, parentenv, handler)
49: lapply(seq_len(cores), inner.do)process_file(text, output)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
50: 16:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)19: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)tryCatchList(expr, classes, parentenv, handlers)
20: 51: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 17: mc.preschedule = TRUE), error = function(e) NULL)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
doTryCatch(return(expr), name, parentenv, handler) output_dir = getwd(), ...)21:
SweepApply(theta, worker, numProcess)
18:
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])vweave_rmarkdown(...)
22:
19: unlist(SweepApply(theta, worker, numProcess))53:
engine$weave(file, quiet = quiet, encoding = enc)tryCatchList(expr, classes, parentenv, handlers)
23: 20: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 54: E = E, showPlot = TRUE) mc.preschedule = TRUE), error = function(e) NULL)
24: doTryCatch(return(expr), name, parentenv, handler)21: eval(expr, envir)SweepApply(theta, worker, numProcess)
22: 55: unlist(SweepApply(theta, worker, numProcess))
tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: 23: eval(expr, envir)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 56: 26: tryCatchList(expr, classes, parentenv, handlers) E = E, showPlot = TRUE)withVisible(eval(expr, envir))
24: 57:
tryCatch({27: eval(expr, envir)withCallingHandlers(code, error = function (e) engine$weave(file, quiet = quiet, encoding = enc)rlang::entrace(e), message = function (cnd) setwd(startdir){
output <- find_vignette_product(name, by = "weave", engine = engine) watcher$capture_plot_and_output()25: if (on_message$capture) {eval(expr, envir) if (!have.makefile && vignette_is_tex(output)) {
watcher$push(cnd)26: texi2pdf(file = output, clean = FALSE, quiet = quiet)withVisible(eval(expr, envir)) } output <- find_vignette_product(name, by = "texi2pdf",
engine = engine) if (on_message$silence) {27: invokeRestart("muffleMessage") }withCallingHandlers(code, error = function (e) } outputs <- c(outputs, output)rlang::entrace(e), message = function (cnd) }, error = function(e) {}, warning = function (cnd) { watcher$capture_plot_and_output() thisOK <<- FALSE if (on_message$capture) {{ watcher$push(cnd) fails <<- c(fails, file) if (getOption("warn") >= 2 || getOption("warn") < 0) { } message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", return() if (on_message$silence) { file, conditionMessage(e))) invokeRestart("muffleMessage") }}) }
58: watcher$capture_plot_and_output()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpbWT6Xp/file8bb456e831d3.rds")}, warning = function (cnd) if (on_warning$capture) {
{ cnd <- sanitize_call(cnd)An irrecoverable exception occurred. R is aborting now ...
if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd) return() } } watcher$capture_plot_and_output() if (on_warning$silence) { if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) invokeRestart("muffleWarning") } if (on_warning$silence) { invokeRestart("muffleWarning") } }}, error = function (cnd) }, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd){ watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL) cnd <- sanitize_call(cnd)})
watcher$push(cnd)28: switch(on_error, continue = invokeRestart("eval_continue"), eval(call) stop = invokeRestart("eval_stop"), error = NULL)
})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$visible, envir)
} TRUE28: }, handlers)eval(call)
31: 29: doWithOneRestart(return(expr), restart)eval(call)
32: 30: withOneRestart(expr, restarts[[1L]])with_handlers({
33: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))withRestartList(expr, restarts[-nr]) watcher$capture_plot_and_output()
34: doWithOneRestart(return(expr), restart) watcher$print_value(ev$value, ev$visible, envir)
}35: TRUEwithOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])}, handlers)
31: 36: doWithOneRestart(return(expr), restart)withRestartList(expr, restarts)
32: 37: withOneRestart(expr, restarts[[1L]])withRestarts(with_handlers({ for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()33: watcher$print_value(ev$value, ev$visible, envir)withRestartList(expr, restarts[-nr]) }
34: TRUEdoWithOneRestart(return(expr), restart)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
35: 38: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])evaluate::evaluate(...)
36: 39: withRestartList(expr, restarts)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 37: keep_message = if (is.numeric(options$message)) TRUE else options$message, withRestarts(with_handlers({ stop_on_error = if (is.numeric(options$error)) options$error else { for (expr in tle$exprs) { if (options$error && options$include) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() 0L watcher$print_value(ev$value, ev$visible, envir) else 2L }, output_handler = knit_handlers(options$render, options)) }
TRUE40: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)in_dir(input_dir(), expr)
38: 41: evaluate::evaluate(...)
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L stop_on_error = if (is.numeric(options$error)) options$error else { else 2L if (options$error && options$include) }, output_handler = knit_handlers(options$render, options)) 0L
else 2L40: }, output_handler = knit_handlers(options$render, options)))in_dir(input_dir(), expr)
41: 42: in_input_dir(evaluate(code, envir = env, new_device = FALSE, eng_r(options) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
43: keep_message = if (is.numeric(options$message)) TRUE else options$message, block_exec(params) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
0L44: else 2Lcall_block(x) }, output_handler = knit_handlers(options$render, options)))
45: 42: process_group(group)eng_r(options)
43: 46: block_exec(params)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {44: if (progress && is.function(pb$interrupt)) call_block(x) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)45: })process_group(group)
47:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 46: error = function(e) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) }), list(rlang_trace_top_env = knit_global())) error <<- format(e) })
48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 47: error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) pb$interrupt() error <<- format(e) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { }), list(rlang_trace_top_env = knit_global())) setwd(wd)
write_utf8(res, output %n% stdout())48: paste0("\nQuitting from ", loc, if (!is.null(error)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), paste0("\n", rule(), error, "\n", rule())) error = function(e) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
if (progress && is.function(pb$interrupt)) 49: pb$interrupt()process_file(text, output) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)51: write_utf8(res, output %n% stdout())rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), paste0("\nQuitting from ", loc, if (!is.null(error)) output_dir = getwd(), ...) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)52:
vweave_rmarkdown(...)49:
process_file(text, output)53: engine$weave(file, quiet = quiet, encoding = enc)
54: 50: doTryCatch(return(expr), name, parentenv, handler)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
55: 51: tryCatchOne(expr, names, parentenv, handlers[[1L]])rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)56:
tryCatchList(expr, classes, parentenv, handlers)52:
vweave_rmarkdown(...)57:
tryCatch({53: engine$weave(file, quiet = quiet, encoding = enc)engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)54: output <- find_vignette_product(name, by = "texi2pdf", doTryCatch(return(expr), name, parentenv, handler) engine = engine)
}55: outputs <- c(outputs, output)tryCatchOne(expr, names, parentenv, handlers[[1L]])}, error = function(e) {
thisOK <<- FALSE56: fails <<- c(fails, file)tryCatchList(expr, classes, parentenv, handlers) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))
57: })tryCatch({
58: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", output <- find_vignette_product(name, by = "weave", engine = engine) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpbWT6Xp/file8bb456e831d3.rds") if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)An irrecoverable exception occurred. R is aborting now ...
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/RtmpbWT6Xp/file8bb456e831d3.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