Last updated on 2026-11-10 01:53:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.2 | 3.43 | 223.65 | 227.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.2 | 2.59 | 222.52 | 225.11 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.2 | OK | ||||
| r-devel-linux-x86_64-fedora-gcc | 2.0.2 | 188.27 | OK | |||
| r-devel-windows-x86_64 | 2.0.2 | 6.00 | 143.00 | 149.00 | OK | |
| r-patched-linux-x86_64 | 2.0.2 | OK | ||||
| r-release-linux-x86_64 | 2.0.2 | 3.34 | 211.51 | 214.85 | OK | |
| r-release-macos-arm64 | 2.0.2 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 2.0.2 | 3.00 | 208.00 | 211.00 | OK | |
| r-release-windows-x86_64 | 2.0.2 | 7.00 | 129.00 | 136.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.2 | 2.00 | 54.00 | 56.00 | 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 | 154.00 | 161.00 | OK |
Version: 2.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-11-10 13:08:43.944 R[49313:73436] 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 ") }
Traceback:
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") 1: .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)RowCumsum(valid) .Internal(printDeferredWarnings())
} 2: invisible(structure(msg, class = "try-error", condition = e))})
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) validLib = validLib, libOverlap = idx$libOverlap, backend = backend,
tieBreak = FALSE, verbose = verbose)14: FUN(X[[i]], ...)
3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, 15: tau = tau, theta = th, exclusionRadius = exclusionRadius, lapply(seq_len(cores), inner.do)
embedded = embedded, validLib = validLib, noTime = noTime, 16: ignoreNan = ignoreNan, backend = backend)parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: 4: ComputeError(predictions$Observations, predictions$Predictions)doTryCatch(return(expr), name, parentenv, handler)
18: 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 19: embedded = embedded, validLib = validLib, noTime = noTime, tryCatchList(expr, classes, parentenv, handlers)
ignoreNan = ignoreNan, backend = backend)$predictions)20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL) 6:
FUN(X[[i]], ...)21: SweepApply(theta, worker, numProcess)
22:
unlist(SweepApply(theta, worker, numProcess)) 7:
lapply(X = S, FUN = FUN, ...)23:
PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 8: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", doTryCatch(return(expr), name, parentenv, handler) E = E, showPlot = TRUE)
24: eval(expr, envir) 9:
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(expr, envir)
10: 26: withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers)
11: 27: tryCatch(expr, error = function(e) {withCallingHandlers(code, error = function (e) call <- conditionCall(e)rlang::entrace(e), message = function (cnd) if (!is.null(call)) {{ if (identical(call[[1L]], quote(doTryCatch))) watcher$capture_plot_and_output() call <- sys.call(-4L) if (on_message$capture) { dcall <- deparse(call, nlines = 1L) watcher$push(cnd) prefix <- paste("Error in", dcall, ": ") } LONG <- 75L if (on_message$silence) { 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") return() if (w > LONG) } watcher$capture_plot_and_output() prefix <- paste0(prefix, "\n ") if (on_warning$capture) { } cnd <- sanitize_call(cnd) watcher$push(cnd) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) if (on_warning$silence) { if (!silent && isTRUE(getOption("show.error.messages"))) { invokeRestart("muffleWarning") cat(msg, file = outFile) .Internal(printDeferredWarnings()) } }}, error = function (cnd) invisible(structure(msg, class = "try-error", condition = e))}){ watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)12: watcher$push(cnd)try(lapply(X = S, FUN = FUN, ...), silent = TRUE) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)})13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
28:
eval(call)14:
FUN(X[[i]], ...)29: eval(call)
30: with_handlers({15: for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))lapply(seq_len(cores), inner.do)
watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) }
TRUE}, handlers)17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)31: doWithOneRestart(return(expr), restart)
20: 32: withOneRestart(expr, restarts[[1L]])tryCatch(parallel::mclapply(values, worker, mc.cores = cores,
mc.preschedule = TRUE), error = function(e) NULL)33:
21: withRestartList(expr, restarts[-nr])
34: SweepApply(theta, worker, numProcess)doWithOneRestart(return(expr), restart)
22: 35: unlist(SweepApply(theta, worker, numProcess))withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", withRestartList(expr, restarts)
E = E, showPlot = TRUE)
37: 24: eval(expr, envir)withRestarts(with_handlers({
for (expr in tle$exprs) {25: ev <- withVisible(eval(expr, envir))
Traceback:
watcher$capture_plot_and_output()eval(expr, envir) watcher$print_value(ev$value, ev$visible, envir) 1: RowCumsum(valid) }
TRUE
26: 2: withVisible(eval(expr, envir))}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
27: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 38: evaluate::evaluate(...) tieBreak = FALSE, verbose = verbose)withCallingHandlers(code, error = function (e)
3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, rlang::entrace(e), message = function (cnd) tau = tau, theta = th, exclusionRadius = exclusionRadius, 39: { embedded = embedded, validLib = validLib, noTime = noTime, watcher$capture_plot_and_output() ignoreNan = ignoreNan, backend = backend)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (on_message$capture) { keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$push(cnd) } stop_on_error = if (is.numeric(options$error)) options$error else { if (on_message$silence) {
if (options$error && options$include) invokeRestart("muffleMessage") 4: } 0L}, warning = function (cnd) ComputeError(predictions$Observations, predictions$Predictions){ else 2L }, output_handler = knit_handlers(options$render, options)) if (getOption("warn") >= 2 || getOption("warn") < 0) {
40: 5: in_dir(input_dir(), expr) return()
}SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, watcher$capture_plot_and_output()41: knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, if (on_warning$capture) {in_input_dir(evaluate(code, envir = env, new_device = FALSE, cnd <- sanitize_call(cnd) embedded = embedded, validLib = validLib, noTime = noTime, watcher$push(cnd) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } ignoreNan = ignoreNan, backend = backend)$predictions) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) if (on_warning$silence) { 0L 6: else 2LFUN(X[[i]], ...) invokeRestart("muffleWarning")
7: }}, error = function (cnd) }, output_handler = knit_handlers(options$render, options)))
lapply(X = S, FUN = FUN, ...){42:
watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) 8: eng_r(options) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), doTryCatch(return(expr), name, parentenv, handler)
43: stop = invokeRestart("eval_stop"), error = NULL) 9: })block_exec(params)tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: 10: tryCatchList(expr, classes, parentenv, handlers)44: eval(call)
call_block(x)11:
tryCatch(expr, error = function(e) {29: 45: eval(call) call <- conditionCall(e)process_group(group)
if (!is.null(call)) {30: 46: with_handlers({withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), for (expr in tle$exprs) { error = function(e) { if (progress && is.function(pb$interrupt)) if (identical(call[[1L]], quote(doTryCatch))) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() call <- sys.call(-4L) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) watcher$print_value(ev$value, ev$visible, envir) } error <<- format(e) dcall <- deparse(call, nlines = 1L) TRUE}, handlers) }) prefix <- paste("Error in", dcall, ": ")
31: LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]]doWithOneRestart(return(expr), restart) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")47: if (is.na(w)) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 32: error = function(e) { type = "b")withOneRestart(expr, restarts[[1L]]) if (progress && is.function(pb$interrupt))
pb$interrupt() if (w > LONG) 33: if (is_R_CMD_build() || is_R_CMD_check()) withRestartList(expr, restarts[-nr])
error <<- format(e)34: }), list(rlang_trace_top_env = knit_global()))
48: doWithOneRestart(return(expr), restart)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 35: prefix <- paste0(prefix, "\n ")withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) } error = function(e) {
if (progress && is.function(pb$interrupt)) else prefix <- "Error : "36: pb$interrupt()withRestartList(expr, restarts)
msg <- paste0(prefix, conditionMessage(e), "\n")37: if (is_R_CMD_build() || is_R_CMD_check()) .Internal(seterrmessage(msg[1L])) error <<- format(e)withRestarts(with_handlers({ if (!silent && isTRUE(getOption("show.error.messages"))) { for (expr in tle$exprs) { }), list(rlang_trace_top_env = knit_global())), function(loc) { cat(msg, file = outFile) ev <- withVisible(eval(expr, envir)) setwd(wd) watcher$capture_plot_and_output() write_utf8(res, output %n% stdout()) .Internal(printDeferredWarnings()) watcher$print_value(ev$value, ev$visible, envir) paste0("\nQuitting from ", loc, if (!is.null(error)) } paste0("\n", rule(), error, "\n", rule())) } invisible(structure(msg, class = "try-error", condition = e))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) TRUE
})49: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
process_file(text, output)
12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)50:
38: 13: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)evaluate::evaluate(...)
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
14: output_dir = getwd(), ...)FUN(X[[i]], ...)39:
52: 15: vweave_rmarkdown(...)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
lapply(seq_len(cores), inner.do)53: keep_message = if (is.numeric(options$message)) TRUE else options$message, engine$weave(file, quiet = quiet, encoding = enc)
16: stop_on_error = if (is.numeric(options$error)) options$error else {parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)54:
doTryCatch(return(expr), name, parentenv, handler)17: if (options$error && options$include) doTryCatch(return(expr), name, parentenv, handler)
0L18: tryCatchOne(expr, names, parentenv, handlers[[1L]])55: else 2L
}, output_handler = knit_handlers(options$render, options))tryCatchOne(expr, names, parentenv, handlers[[1L]])19:
40: 56: in_dir(input_dir(), expr)tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
20: 41: 57: in_input_dir(evaluate(code, envir = env, new_device = FALSE, tryCatch(parallel::mclapply(values, worker, mc.cores = cores, tryCatch({ keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, mc.preschedule = TRUE), error = function(e) NULL)
engine$weave(file, quiet = quiet, encoding = enc) keep_message = if (is.numeric(options$message)) TRUE else options$message, 21: stop_on_error = if (is.numeric(options$error)) options$error else {SweepApply(theta, worker, numProcess) setwd(startdir)
if (options$error && options$include) output <- find_vignette_product(name, by = "weave", engine = engine)22: 0L if (!have.makefile && vignette_is_tex(output)) { else 2L texi2pdf(file = output, clean = FALSE, quiet = quiet)unlist(SweepApply(theta, worker, numProcess)) }, output_handler = knit_handlers(options$render, options))) output <- find_vignette_product(name, by = "texi2pdf",
Traceback:
23: engine = engine) 1: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", } outputs <- c(outputs, output)42: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", eng_r(options)RowCumsum(valid)}, error = function(e) {
2: thisOK <<- FALSEFindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius,
E = E, showPlot = TRUE)43: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, block_exec(params)
24: tieBreak = FALSE, verbose = verbose)eval(expr, envir) fails <<- c(fails, file)
25: 44: message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
eval(expr, envir) file, conditionMessage(e))) 3: call_block(x)})
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn,
26: 45: withVisible(eval(expr, envir))58: tau = tau, theta = th, exclusionRadius = exclusionRadius,
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", embedded = embedded, validLib = validLib, noTime = noTime, 27: ignoreNan = ignoreNan, backend = backend)withCallingHandlers(code, error = function (e) process_group(group)
rlang::entrace(e), message = function (cnd) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpVAGaEE/file91987dcbfacd.rds"){ 4:
watcher$capture_plot_and_output()46: if (on_message$capture) {withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { watcher$push(cnd)
ComputeError(predictions$Observations, predictions$Predictions) if (progress && is.function(pb$interrupt)) }
if (on_message$silence) {An irrecoverable exception occurred. R is aborting now ...
invokeRestart("muffleMessage") pb$interrupt() 5: } if (is_R_CMD_build() || is_R_CMD_check()) SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, }, warning = function (cnd) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, error <<- format(e) embedded = embedded, validLib = validLib, noTime = noTime, }){ ignoreNan = ignoreNan, backend = backend)$predictions) if (getOption("warn") >= 2 || getOption("warn") < 0) {
6: 47: return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd)FUN(X[[i]], ...)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$push(cnd) }
error = function(e) { if (on_warning$silence) { 7: if (progress && is.function(pb$interrupt)) invokeRestart("muffleWarning")lapply(X = S, FUN = FUN, ...) }
pb$interrupt()}, error = function (cnd) 8: doTryCatch(return(expr), name, parentenv, handler) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e){
}), list(rlang_trace_top_env = knit_global())) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$capture_plot_and_output()48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), cnd <- sanitize_call(cnd)10: error = function(e) { watcher$push(cnd)tryCatchList(expr, classes, parentenv, handlers) if (progress && is.function(pb$interrupt)) switch(on_error, continue = invokeRestart("eval_continue"), pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) stop = invokeRestart("eval_stop"), error = NULL) error <<- format(e)11: }) }), list(rlang_trace_top_env = knit_global())), function(loc) {tryCatch(expr, error = function(e) {
setwd(wd)28: call <- conditionCall(e) write_utf8(res, output %n% stdout()) if (!is.null(call)) { paste0("\nQuitting from ", loc, if (!is.null(error)) eval(call) paste0("\n", rule(), error, "\n", rule())) if (identical(call[[1L]], quote(doTryCatch))) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
call <- sys.call(-4L)
29: dcall <- deparse(call, nlines = 1L)eval(call)49: prefix <- paste("Error in", dcall, ": ")
process_file(text, output)30: LONG <- 75L
with_handlers({ sm <- strsplit(conditionMessage(e), "\n")[[1L]]50: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") for (expr in tle$exprs) {knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ev <- withVisible(eval(expr, envir))51: type = "b") watcher$capture_plot_and_output() if (w > LONG) prefix <- paste0(prefix, "\n ")rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), } watcher$print_value(ev$value, ev$visible, envir) output_dir = getwd(), ...) }
TRUE52: }, handlers)vweave_rmarkdown(...) else prefix <- "Error : "
53:
31: msg <- paste0(prefix, conditionMessage(e), "\n")doWithOneRestart(return(expr), restart) .Internal(seterrmessage(msg[1L]))engine$weave(file, quiet = quiet, encoding = enc) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings())
32: }withOneRestart(expr, restarts[[1L]])54: invisible(structure(msg, class = "try-error", condition = e))doTryCatch(return(expr), name, parentenv, handler)
})33: 55:
withRestartList(expr, restarts[-nr])tryCatchOne(expr, names, parentenv, handlers[[1L]])
12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)56: 34:
tryCatchList(expr, classes, parentenv, handlers)doWithOneRestart(return(expr), restart)
57: 13: 35: tryCatch({withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) engine$weave(file, quiet = quiet, encoding = enc)
36: 14: setwd(startdir)withRestartList(expr, restarts) output <- find_vignette_product(name, by = "weave", engine = engine)FUN(X[[i]], ...)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)15: output <- find_vignette_product(name, by = "texi2pdf", 37: engine = engine)lapply(seq_len(cores), inner.do)withRestarts(with_handlers({
} for (expr in tle$exprs) {16: outputs <- c(outputs, output) ev <- withVisible(eval(expr, envir))}, error = function(e) { watcher$capture_plot_and_output() thisOK <<- FALSEparallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) watcher$print_value(ev$value, ev$visible, envir) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }
17: file, conditionMessage(e)))doTryCatch(return(expr), name, parentenv, handler)}) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)58:
18: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", tryCatchOne(expr, names, parentenv, handlers[[1L]]) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpVAGaEE/file91987dcbfacd.rds")
19: 38: tryCatchList(expr, classes, parentenv, handlers)
An irrecoverable exception occurred. R is aborting now ...
evaluate::evaluate(...)20:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 39: mc.preschedule = TRUE), error = function(e) NULL)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) 21: 0LSweepApply(theta, worker, numProcess) else 2L
22: }, output_handler = knit_handlers(options$render, options))unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", 40: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, E = E, showPlot = TRUE)
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 24: keep_message = if (is.numeric(options$message)) TRUE else options$message, eval(expr, envir) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 25: eval(expr, envir)
0L26: withVisible(eval(expr, envir)) else 2L
}, output_handler = knit_handlers(options$render, options)))27:
withCallingHandlers(code, error = function (e) 42: rlang::entrace(e), message = function (cnd) eng_r(options){
watcher$capture_plot_and_output()43: if (on_message$capture) {block_exec(params) watcher$push(cnd)
}44: if (on_message$silence) {call_block(x) invokeRestart("muffleMessage")
45: }process_group(group)}, warning = function (cnd) {
if (getOption("warn") >= 2 || getOption("warn") < 0) {46: return()withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) if (on_warning$capture) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) cnd <- sanitize_call(cnd) }) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning")
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) {}, error = function (cnd) if (progress && is.function(pb$interrupt)) pb$interrupt(){ if (is_R_CMD_build() || is_R_CMD_check()) watcher$capture_plot_and_output() error <<- format(e) cnd <- sanitize_call(cnd) }), list(rlang_trace_top_env = knit_global()))
watcher$push(cnd)48: switch(on_error, continue = invokeRestart("eval_continue"), xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop = invokeRestart("eval_stop"), error = NULL) error = function(e) {})
if (progress && is.function(pb$interrupt)) 28: pb$interrupt()eval(call) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)29: eval(call) }), 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)
30: 49: with_handlers({process_file(text, output) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))50: watcher$capture_plot_and_output()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$print_value(ev$value, ev$visible, envir)
}51: TRUErmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }, handlers) output_dir = getwd(), ...)
31: doWithOneRestart(return(expr), restart)52:
vweave_rmarkdown(...)
32: 53: withOneRestart(expr, restarts[[1L]])engine$weave(file, quiet = quiet, encoding = enc)
54:
33: doTryCatch(return(expr), name, parentenv, handler)withRestartList(expr, restarts[-nr])
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])34:
doWithOneRestart(return(expr), restart)56: tryCatchList(expr, classes, parentenv, handlers)
35: 57: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)36: output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) {withRestartList(expr, restarts) texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf", 37: engine = engine)withRestarts(with_handlers({ for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir)) outputs <- c(outputs, output) watcher$capture_plot_and_output()}, error = function(e) { watcher$print_value(ev$value, ev$visible, envir) thisOK <<- FALSE } fails <<- c(fails, file) TRUE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) file, conditionMessage(e)))
})38:
evaluate::evaluate(...)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/RtmpVAGaEE/file91987dcbfacd.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, 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/RtmpVAGaEE/file91987dcbfacd.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