Last updated on 2026-08-16 12:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.57 | 226.18 | 229.75 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.11 | 237.63 | 239.74 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 4.00 | 257.00 | 261.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.27 | 210.37 | 213.64 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 0.00 | 6.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 43.00 | 44.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 8.00 | 165.00 | 173.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-16 21:12:04.225 R[42009:61031] 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$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 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, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$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]], ...)
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") 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) 9: .Internal(printDeferredWarnings()) }tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers) invisible(structure(msg, class = "try-error", condition = e))})
11:
12: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...) 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)
Traceback:
17: 1: RowCumsum(valid)doTryCatch(return(expr), name, parentenv, handler)
18: 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
lapply(seq_len(cores), inner.do)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)16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: 2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
22: unlist(SweepApply(theta, worker, numProcess))
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, 23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", ignoreNan = ignoreNan, backend = backend) target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: ComputeError(predictions$Observations, predictions$Predictions)
24: eval(expr, envir)
25: eval(expr, envir)
5: 19: tryCatchList(expr, classes, parentenv, handlers)SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8:
26:
doTryCatch(return(expr), name, parentenv, handler)withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }
}, warning = function (cnd) { 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) { mc.preschedule = TRUE), error = function(e) NULL) return()
11: } watcher$capture_plot_and_output()tryCatch(expr, error = function(e) {
call <- conditionCall(e) if (on_warning$capture) {21: if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) cnd <- sanitize_call(cnd) watcher$push(cnd)
Traceback:
} if (on_warning$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$exprs) { ev <- withVisible(eval(expr, envir)) call <- sys.call(-4L)SweepApply(theta, worker, numProcess) watcher$capture_plot_and_output() 1:
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)) RowCumsum(valid) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) watcher$print_value(ev$value, ev$visible, envir)22: } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
32: prefix <- paste0(prefix, "\n ")withOneRestart(expr, restarts[[1L]])
} else prefix <- "Error : "33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
unlist(SweepApply(theta, worker, numProcess))
msg <- paste0(prefix, conditionMessage(e), "\n")
23: 2: .Internal(seterrmessage(msg[1L]))FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, 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, if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings())PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", ignoreNan = ignoreNan, backend = backend)
} 4: target = "Thrips_imaginis", lib = "1 73", pred = "1 73", invisible(structure(msg, class = "try-error", condition = e)) E = E, showPlot = TRUE)
24: eval(expr, envir)
25: 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, 35: }) embedded = embedded, validLib = validLib, noTime = noTime,
eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()12: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (on_message$capture) { ignoreNan = ignoreNan, backend = backend)$predictions)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
watcher$push(cnd) 6: } if (on_message$silence) { invokeRestart("muffleMessage")
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({ }}, warning = function (cnd) {13: if (getOption("warn") >= 2 || getOption("warn") < 0) { for (expr in tle$exprs) {sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
14: FUN(X[[i]], ...)
} 7: lapply(X = S, FUN = FUN, ...)15: return()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)) TRUE 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) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE){ watcher$capture_plot_and_output()23: cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 8: doTryCatch(return(expr), name, parentenv, handler)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73",
38: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 28:
eval(call) 9:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { E = E, showPlot = TRUE)
29: 10: tryCatchList(expr, classes, parentenv, handlers)
11: 24: if (options$error && options$include) tryCatch(expr, error = function(e) {eval(expr, envir)eval(call) call <- conditionCall(e)
if (!is.null(call)) {25: if (identical(call[[1L]], quote(doTryCatch))) 0L call <- sys.call(-4L) else 2L dcall <- deparse(call, nlines = 1L) }, output_handler = knit_handlers(options$render, options))
prefix <- paste("Error in", dcall, ": ") LONG <- 75Leval(expr, envir)30: with_handlers({ sm <- strsplit(conditionMessage(e), "\n")[[1L]]
40: in_dir(input_dir(), expr)
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include) 0L for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, handlers)
if (is.na(w)) 31: 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"))) { else 2LdoWithOneRestart(return(expr), restart) cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) }, output_handler = knit_handlers(options$render, options)))
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: 26: 32: withOneRestart(expr, restarts[[1L]])
33:
withVisible(eval(expr, envir))42: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))eng_r(options)
withRestartList(expr, restarts[-nr])
27: 43: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()34: if (on_message$capture) {doWithOneRestart(return(expr), restart) watcher$push(cnd)
block_exec(params)
14: 44: call_block(x)
}FUN(X[[i]], ...)
if (on_message$silence) {
invokeRestart("muffleMessage")15: 45: }}, warning = function (cnd) 35: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), lapply(seq_len(cores), inner.do){
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) error = function(e) { if (getOption("warn") >= 2 || getOption("warn") < 0) {doTryCatch(return(expr), name, parentenv, handler) if (progress && is.function(pb$interrupt)) return() }
pb$interrupt()
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
watcher$capture_plot_and_output()36: 20: if (is_R_CMD_build() || is_R_CMD_check()) tryCatch(parallel::mclapply(values, worker, mc.cores = cores, if (on_warning$capture) { mc.preschedule = TRUE), error = function(e) NULL)
withRestartList(expr, restarts) cnd <- sanitize_call(cnd) error <<- format(e)21: }), list(rlang_trace_top_env = knit_global()))
watcher$push(cnd)SweepApply(theta, worker, numProcess)
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$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...) }
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 39: error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }), list(rlang_trace_top_env = knit_global())), function(loc) { if (on_warning$silence) { keep_message = if (is.numeric(options$message)) TRUE else options$message, setwd(wd)22: stop_on_error = if (is.numeric(options$error)) options$error else { write_utf8(res, output %n% stdout()) invokeRestart("muffleWarning") paste0("\nQuitting from ", loc, if (!is.null(error)) 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)
if (options$error && options$include) 0L }}, error = function (cnd) else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
{
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))50: 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: 24: eval(expr, envir)
25: eval(expr, envir)
eval(call)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
26: 29: withVisible(eval(expr, envir))eval(call)
30: with_handlers({42:
eng_r(options)51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd)
43: for (expr in tle$exprs) {{ ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
watcher$capture_plot_and_output()52: vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc)
block_exec(params) if (on_message$capture) { watcher$push(cnd)54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
}
56: 32: withOneRestart(expr, restarts[[1L]]) if (on_message$silence) {44: call_block(x)
33: invokeRestart("muffleMessage")withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
57:
tryCatch({34: 45: }process_group(group) engine$weave(file, quiet = quiet, encoding = enc)doWithOneRestart(return(expr), restart)}, warning = function (cnd)
{35: 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) setwd(startdir) if (getOption("warn") >= 2 || getOption("warn") < 0) { return() pb$interrupt() }
watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) {36: output <- find_vignette_product(name, by = "weave", engine = engine) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }withRestartList(expr, restarts)
invokeRestart("muffleWarning")37: outputs <- c(outputs, output)withRestarts(with_handlers({}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }) } for (expr in tle$exprs) {}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) ev <- withVisible(eval(expr, envir))
47: switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) file, conditionMessage(e)))})
watcher$capture_plot_and_output()28: }) watcher$print_value(ev$value, ev$visible, envir)
}eval(call)58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpJn6px6/file6ad824a96db5.rds")
An irrecoverable exception occurred. R is aborting now ...
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) { TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: setwd(wd)evaluate::evaluate(...)
29: eval(call)
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$warning, write_utf8(res, output %n% stdout()) keep_message = if (is.numeric(options$message)) TRUE else options$message, paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L30: with_handlers({ for (expr in tle$exprs) {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) ev <- withVisible(eval(expr, envir))
49: watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) else 2Lprocess_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: }, output_handler = knit_handlers(options$render, options)))
42: vweave_rmarkdown(...)
53: }engine$weave(file, quiet = quiet, encoding = enc)
eng_r(options)54: doTryCatch(return(expr), name, parentenv, handler)
55: TRUE}, handlers)
31: doWithOneRestart(return(expr), restart)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: withOneRestart(expr, restarts[[1L]])block_exec(params)
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: 44: 56: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)call_block(x) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)
45: process_group(group)
37: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) output <- find_vignette_product(name, by = "texi2pdf", 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { engine = engine) } outputs <- c(outputs, output) if (progress && is.function(pb$interrupt)) }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
watcher$capture_plot_and_output()47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), file, conditionMessage(e))) error = function(e) { watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38: evaluate::evaluate(...)
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())
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/RtmpJn6px6/file6ad824a96db5.rds")
An irrecoverable exception occurred. R is aborting now ...
error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) {39: 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: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, process_file(text, output) keep_message = if (is.numeric(options$message)) TRUE else options$message,
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$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers) stop_on_error = if (is.numeric(options$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:
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpJn6px6/file6ad824a96db5.rds")
An irrecoverable exception occurred. R is aborting now ...
keep_message = if (is.numeric(options$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)))
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/RtmpJn6px6/file6ad824a96db5.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