Last updated on 2026-09-29 12:50:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.19 | 226.61 | 229.80 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.52 | 224.17 | 226.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | 175.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 189.12 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 4.00 | 139.00 | 143.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | 3.72 | 205.17 | 208.89 | OK | |
| r-release-linux-x86_64 | 2.0.2 | 3.56 | 209.84 | 213.40 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 6.00 | 130.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 1.00 | 38.00 | 39.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.2 | 3.00 | 201.00 | 204.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.2 | 8.00 | 158.00 | 166.00 | 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
2026-09-29 19:14:41.379 R[42851:63923] 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:
Traceback:
lapply(seq_len(cores), inner.do)
1: 16: RowCumsum(valid)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
2: 17: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, doTryCatch(return(expr), name, parentenv, handler) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 19: tryCatchList(expr, classes, parentenv, handlers) ignoreNan = ignoreNan, backend = backend)
4: 20: ComputeError(predictions$Observations, predictions$Predictions)tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL) 5:
SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 21: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, SweepApply(theta, worker, numProcess) embedded = embedded, validLib = validLib, noTime = noTime,
ignoreNan = ignoreNan, backend = backend)$predictions)22:
unlist(SweepApply(theta, worker, numProcess)) 6:
23: FUN(X[[i]], ...)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) 7:
lapply(X = S, FUN = FUN, ...)24:
eval(expr, envir) 8:
doTryCatch(return(expr), name, parentenv, handler)25:
eval(expr, envir) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]])26:
withVisible(eval(expr, envir))10:
tryCatchList(expr, classes, parentenv, handlers)27:
withCallingHandlers(code, error = function (e) 11: rlang::entrace(e), message = function (cnd) tryCatch(expr, error = function(e) {{ call <- conditionCall(e) watcher$capture_plot_and_output() if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) if (on_message$capture) { call <- sys.call(-4L) watcher$push(cnd) } dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") if (on_message$silence) { LONG <- 75L invokeRestart("muffleMessage") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, warning = function (cnd) if (is.na(w)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (getOption("warn") >= 2 || getOption("warn") < 0) { type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") return()
Traceback:
} } else prefix <- "Error : " 1: watcher$capture_plot_and_output() msg <- paste0(prefix, conditionMessage(e), "\n")RowCumsum(valid) if (on_warning$capture) {
.Internal(seterrmessage(msg[1L])) cnd <- sanitize_call(cnd) 2: watcher$push(cnd)FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, } if (!silent && isTRUE(getOption("show.error.messages"))) { if (on_warning$silence) { cat(msg, file = outFile) validLib = validLib, libOverlap = idx$libOverlap, backend = backend, .Internal(printDeferredWarnings()) invokeRestart("muffleWarning") tieBreak = FALSE, verbose = verbose) }
invisible(structure(msg, class = "try-error", condition = e)) }}) 3: }, error = function (cnd)
{SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, watcher$capture_plot_and_output() tau = tau, theta = th, exclusionRadius = exclusionRadius, 12: cnd <- sanitize_call(cnd)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) embedded = embedded, validLib = validLib, noTime = noTime, watcher$push(cnd) ignoreNan = ignoreNan, backend = backend) switch(on_error, continue = invokeRestart("eval_continue"),
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
stop = invokeRestart("eval_stop"), error = NULL) 4: 14: })ComputeError(predictions$Observations, predictions$Predictions)
FUN(X[[i]], ...)
28:
5: eval(call)15:
lapply(seq_len(cores), inner.do)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 29: embedded = embedded, validLib = validLib, noTime = noTime, eval(call)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)30: ignoreNan = ignoreNan, backend = backend)$predictions)
with_handlers({17: for (expr in tle$exprs) {
doTryCatch(return(expr), name, parentenv, handler) 6: ev <- withVisible(eval(expr, envir))FUN(X[[i]], ...)
watcher$capture_plot_and_output() 7: watcher$print_value(ev$value, ev$visible, envir)lapply(X = S, FUN = FUN, ...) }18: TRUE
}, handlers) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])doTryCatch(return(expr), name, parentenv, handler)
31: 19: 9: doWithOneRestart(return(expr), restart)tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
10: 32:
tryCatchList(expr, classes, parentenv, handlers)withOneRestart(expr, restarts[[1L]])
20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 33: mc.preschedule = TRUE), error = function(e) NULL)withRestartList(expr, restarts[-nr])11:
tryCatch(expr, error = function(e) {
call <- conditionCall(e)34: 21: if (!is.null(call)) {doWithOneRestart(return(expr), restart)SweepApply(theta, worker, numProcess)
if (identical(call[[1L]], quote(doTryCatch))) 35: call <- sys.call(-4L)22: dcall <- deparse(call, nlines = 1L)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) prefix <- paste("Error in", dcall, ": ")unlist(SweepApply(theta, worker, numProcess)) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]23: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", if (is.na(w)) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 36: E = E, showPlot = TRUE) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")24: withRestartList(expr, restarts)eval(expr, envir) if (w > LONG)
prefix <- paste0(prefix, "\n ")37: 25: }withRestarts(with_handlers({ else prefix <- "Error : " for (expr in tle$exprs) {eval(expr, envir) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) ev <- withVisible(eval(expr, envir)) if (!silent && isTRUE(getOption("show.error.messages"))) { watcher$capture_plot_and_output() cat(msg, file = outFile)26: .Internal(printDeferredWarnings()) watcher$print_value(ev$value, ev$visible, envir)withVisible(eval(expr, envir)) } invisible(structure(msg, class = "try-error", condition = e)) }})
TRUE27:
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)withCallingHandlers(code, error = function (e) 12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)rlang::entrace(e), message = function (cnd) 38:
{evaluate::evaluate(...)
13: watcher$capture_plot_and_output()sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) if (on_message$capture) {39: watcher$push(cnd)
}evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_message$silence) {14: invokeRestart("muffleMessage")FUN(X[[i]], ...)
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) }, warning = function (cnd) 15: { 0Llapply(seq_len(cores), inner.do) if (getOption("warn") >= 2 || getOption("warn") < 0) { else 2L return()
}, output_handler = knit_handlers(options$render, options)) }
16: watcher$capture_plot_and_output()40: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) if (on_warning$capture) {
in_dir(input_dir(), expr) cnd <- sanitize_call(cnd)
17: watcher$push(cnd) }41: doTryCatch(return(expr), name, parentenv, handler)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
if (on_warning$silence) {18: invokeRestart("muffleWarning")tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
Traceback:
} keep_message = if (is.numeric(options$message)) TRUE else options$message, }, error = function (cnd)
1: {19: stop_on_error = if (is.numeric(options$error)) options$error else {tryCatchList(expr, classes, parentenv, handlers)RowCumsum(valid)
watcher$capture_plot_and_output()
if (options$error && options$include) 2: cnd <- sanitize_call(cnd)20: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, watcher$push(cnd)tryCatch(parallel::mclapply(values, worker, mc.cores = cores, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, mc.preschedule = TRUE), error = function(e) NULL) 0L
switch(on_error, continue = invokeRestart("eval_continue"), 21: tieBreak = FALSE, verbose = verbose) stop = invokeRestart("eval_stop"), error = NULL)
SweepApply(theta, worker, numProcess) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 22: tau = tau, theta = th, exclusionRadius = exclusionRadius, })unlist(SweepApply(theta, worker, numProcess))
else 2L28:
embedded = embedded, validLib = validLib, noTime = noTime, }, output_handler = knit_handlers(options$render, options)))23: ignoreNan = ignoreNan, backend = backend)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", 42: eval(call) 4: E = E, showPlot = TRUE)
eng_r(options)29:
eval(call)
24: ComputeError(predictions$Observations, predictions$Predictions)eval(expr, envir)30:
43: with_handlers({
25: for (expr in tle$exprs) { 5: eval(expr, envir)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, ev <- withVisible(eval(expr, envir)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, block_exec(params)
embedded = embedded, validLib = validLib, noTime = noTime,
watcher$capture_plot_and_output() ignoreNan = ignoreNan, backend = backend)$predictions)44: watcher$print_value(ev$value, ev$visible, envir)
call_block(x)26: }withVisible(eval(expr, envir)) 6:
FUN(X[[i]], ...)
TRUE45: 27: process_group(group)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) }, handlers)46: {
7: watcher$capture_plot_and_output()31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), lapply(X = S, FUN = FUN, ...) if (on_message$capture) {doWithOneRestart(return(expr), restart) error = function(e) {
if (progress && is.function(pb$interrupt)) 32: 8: watcher$push(cnd)withOneRestart(expr, restarts[[1L]]) }doTryCatch(return(expr), name, parentenv, handler) pb$interrupt()
if (on_message$silence) { 9:
if (is_R_CMD_build() || is_R_CMD_check()) tryCatchOne(expr, names, parentenv, handlers[[1L]])33: withRestartList(expr, restarts[-nr])
invokeRestart("muffleMessage") error <<- format(e)
}10: 34: })tryCatchList(expr, classes, parentenv, handlers)}, warning = function (cnd) doWithOneRestart(return(expr), restart)
{47: 35: 11: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatch(expr, error = function(e) { if (getOption("warn") >= 2 || getOption("warn") < 0) { call <- conditionCall(e)
if (!is.null(call)) {36: return() if (identical(call[[1L]], quote(doTryCatch))) withRestartList(expr, restarts) error = function(e) { call <- sys.call(-4L) } if (progress && is.function(pb$interrupt)) dcall <- deparse(call, nlines = 1L) watcher$capture_plot_and_output()
if (on_warning$capture) { prefix <- paste("Error in", dcall, ": ") pb$interrupt()37: LONG <- 75LwithRestarts(with_handlers({ sm <- strsplit(conditionMessage(e), "\n")[[1L]] for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") cnd <- sanitize_call(cnd) error <<- format(e) ev <- withVisible(eval(expr, envir)) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$print_value(ev$value, ev$visible, envir) watcher$push(cnd) }), list(rlang_trace_top_env = knit_global())) }
}48: TRUE if (on_warning$silence) {}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) type = "b") invokeRestart("muffleWarning")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }
if (w > LONG) error = function(e) {}, error = function (cnd) prefix <- paste0(prefix, "\n "){ } watcher$capture_plot_and_output()38: cnd <- sanitize_call(cnd)evaluate::evaluate(...) else prefix <- "Error : " watcher$push(cnd) if (progress && is.function(pb$interrupt))
pb$interrupt() switch(on_error, continue = invokeRestart("eval_continue"), if (is_R_CMD_build() || is_R_CMD_check()) 39: error <<- format(e) msg <- paste0(prefix, conditionMessage(e), "\n") stop = invokeRestart("eval_stop"), error = NULL) .Internal(seterrmessage(msg[1L])) }), list(rlang_trace_top_env = knit_global())), function(loc) { if (!silent && isTRUE(getOption("show.error.messages"))) { setwd(wd)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, write_utf8(res, output %n% stdout()) cat(msg, file = outFile) paste0("\nQuitting from ", loc, if (!is.null(error)) }) .Internal(printDeferredWarnings()) paste0("\n", rule(), error, "\n", rule()))
keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { invisible(structure(msg, class = "try-error", condition = e))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)})
28: 12: if (options$error && options$include) eval(call)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)49:
0L29: process_file(text, output)
else 2L13: eval(call)
}, output_handler = knit_handlers(options$render, options))50: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)14: 40: FUN(X[[i]], ...)30: in_dir(input_dir(), expr)
with_handlers({41: 15: in_input_dir(evaluate(code, envir = env, new_device = FALSE, for (expr in tle$exprs) {lapply(seq_len(cores), inner.do) ev <- withVisible(eval(expr, envir))
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 51: watcher$capture_plot_and_output()
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), watcher$print_value(ev$value, ev$visible, envir) 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) TRUE output_dir = getwd(), ...)}, handlers)16:
parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)52: 31:
0Lvweave_rmarkdown(...)17:
else 2LdoWithOneRestart(return(expr), restart)doTryCatch(return(expr), name, parentenv, handler) }, output_handler = knit_handlers(options$render, options)))
53: 18: engine$weave(file, quiet = quiet, encoding = enc)32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
withOneRestart(expr, restarts[[1L]])
42:
19: eng_r(options)
tryCatchList(expr, classes, parentenv, handlers)33:
withRestartList(expr, restarts[-nr])43:
54:
20: 34: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, block_exec(params)doTryCatch(return(expr), name, parentenv, handler) mc.preschedule = TRUE), error = function(e) NULL)doWithOneRestart(return(expr), restart)
44: 55: 21: 35: tryCatchOne(expr, names, parentenv, handlers[[1L]])call_block(x)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])SweepApply(theta, worker, numProcess)
56: 22: tryCatchList(expr, classes, parentenv, handlers)45: unlist(SweepApply(theta, worker, numProcess))36:
withRestartList(expr, restarts)57: 23: tryCatch({process_group(group)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", engine$weave(file, quiet = quiet, encoding = enc)
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", setwd(startdir) E = E, showPlot = TRUE)37:
output <- find_vignette_product(name, by = "weave", engine = engine)24:
withRestarts(with_handlers({ if (!have.makefile && vignette_is_tex(output)) {46: eval(expr, envir) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), texi2pdf(file = output, clean = FALSE, quiet = quiet) watcher$capture_plot_and_output()25: watcher$print_value(ev$value, ev$visible, envir) output <- find_vignette_product(name, by = "texi2pdf", eval(expr, envir) } error = function(e) { engine = engine) TRUE
if (progress && is.function(pb$interrupt)) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }
26: outputs <- c(outputs, output) pb$interrupt()}, error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) withVisible(eval(expr, envir)) error <<- format(e)38: thisOK <<- FALSE
fails <<- c(fails, file) })27: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", evaluate::evaluate(...)
withCallingHandlers(code, error = function (e) file, conditionMessage(e)))47: })
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 39: rlang::entrace(e), message = function (cnd)
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 58: {tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", error = function(e) { watcher$capture_plot_and_output() skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2Fw963/file81695d5cc7b1.rds") keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else { if (progress && is.function(pb$interrupt)) if (on_message$capture) {An irrecoverable exception occurred. R is aborting now ...
if (options$error && options$include) watcher$push(cnd) pb$interrupt() } 0L if (is_R_CMD_build() || is_R_CMD_check()) else 2L if (on_message$silence) { }, output_handler = knit_handlers(options$render, options)) error <<- format(e) invokeRestart("muffleMessage")
}40: }), list(rlang_trace_top_env = knit_global()))}, warning = function (cnd) in_dir(input_dir(), expr){
if (getOption("warn") >= 2 || getOption("warn") < 0) {
41: return() }in_input_dir(evaluate(code, envir = env, new_device = FALSE, watcher$capture_plot_and_output() keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_warning$capture) {48: cnd <- sanitize_call(cnd) keep_message = if (is.numeric(options$message)) TRUE else options$message, xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop_on_error = if (is.numeric(options$error)) options$error else { error = function(e) { watcher$push(cnd) if (options$error && options$include) } if (progress && is.function(pb$interrupt)) if (on_warning$silence) { 0L pb$interrupt() else 2L if (is_R_CMD_build() || is_R_CMD_check()) invokeRestart("muffleWarning") error <<- format(e) }, output_handler = knit_handlers(options$render, options))) } }), list(rlang_trace_top_env = knit_global())), function(loc) {
}, error = function (cnd) setwd(wd){42: write_utf8(res, output %n% stdout()) watcher$capture_plot_and_output()eng_r(options) paste0("\nQuitting from ", loc, if (!is.null(error)) cnd <- sanitize_call(cnd)
paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$push(cnd)
43: switch(on_error, continue = invokeRestart("eval_continue"), 49: stop = invokeRestart("eval_stop"), error = NULL)})block_exec(params)
process_file(text, output)28:
eval(call)50: 44: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
call_block(x)29:
51: 45: eval(call)process_group(group)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
30: output_dir = getwd(), ...)with_handlers({46: for (expr in tle$exprs) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output() error = function(e) { watcher$print_value(ev$value, ev$visible, envir)52: if (progress && is.function(pb$interrupt)) vweave_rmarkdown(...) pb$interrupt() } if (is_R_CMD_build() || is_R_CMD_check()) TRUE
error <<- format(e)}, handlers) })
53: 31: engine$weave(file, quiet = quiet, encoding = enc)
doWithOneRestart(return(expr), restart)47:
54: 32: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withOneRestart(expr, restarts[[1L]])doTryCatch(return(expr), name, parentenv, handler)
error = function(e) {
33: 55: if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr]) pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)56: }), list(rlang_trace_top_env = knit_global()))
tryCatchList(expr, classes, parentenv, handlers)
34: 48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 57: doWithOneRestart(return(expr), restart) error = function(e) {tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)35: setwd(startdir) if (progress && is.function(pb$interrupt)) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) pb$interrupt() output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { if (is_R_CMD_build() || is_R_CMD_check()) texi2pdf(file = output, clean = FALSE, quiet = quiet)36: output <- find_vignette_product(name, by = "texi2pdf", error <<- format(e) engine = engine) }), list(rlang_trace_top_env = knit_global())), function(loc) { } setwd(wd)withRestartList(expr, restarts) outputs <- c(outputs, output)
}, error = function(e) { write_utf8(res, output %n% stdout()) thisOK <<- FALSE37: fails <<- c(fails, file)withRestarts(with_handlers({ message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", paste0("\nQuitting from ", loc, if (!is.null(error)) for (expr in tle$exprs) { file, conditionMessage(e))) ev <- withVisible(eval(expr, envir)) paste0("\n", rule(), error, "\n", rule())) watcher$capture_plot_and_output()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$print_value(ev$value, ev$visible, envir)
}49: })process_file(text, output)
50: TRUEknitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)58:
38: 51: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", evaluate::evaluate(...)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2Fw963/file81695d5cc7b1.rds")39:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
An irrecoverable exception occurred. R is aborting now ...
keep_message = if (is.numeric(options$message)) TRUE else options$message, 52: stop_on_error = if (is.numeric(options$error)) options$error else {vweave_rmarkdown(...) if (options$error && options$include)
0L53: else 2Lengine$weave(file, quiet = quiet, encoding = enc) }, output_handler = knit_handlers(options$render, options))
54: 40: doTryCatch(return(expr), name, parentenv, handler)in_dir(input_dir(), expr)
55: 41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
56: keep_message = if (is.numeric(options$message)) TRUE else options$message, tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 57: 0L else 2LtryCatch({ }, output_handler = knit_handlers(options$render, options))) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)42: output <- find_vignette_product(name, by = "weave", engine = engine)eng_r(options) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)43: output <- find_vignette_product(name, by = "texi2pdf", block_exec(params) engine = engine)
}44: outputs <- c(outputs, output)call_block(x)
}, error = function(e) {45: thisOK <<- FALSEprocess_group(group) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 46: file, conditionMessage(e)))withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) {
if (progress && is.function(pb$interrupt)) 58: pb$interrupt()tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", if (is_R_CMD_build() || is_R_CMD_check()) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp2Fw963/file81695d5cc7b1.rds") error <<- format(e)
})An irrecoverable exception occurred. R is aborting now ...
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/Rtmp2Fw963/file81695d5cc7b1.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