Last updated on 2026-10-20 01:50:13 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 4.45 | 65.19 | 69.64 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.23 | 50.96 | 54.19 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 46.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 55.06 | OK | |||
| r-devel-windows-x86_64 | 1.2.3 | 7.00 | 129.00 | 136.00 | OK | |
| r-patched-linux-x86_64 | 1.2.3 | 3.85 | 60.42 | 64.27 | OK | |
| r-release-linux-x86_64 | 1.2.3 | 4.29 | 59.97 | 64.26 | OK | |
| r-release-macos-arm64 | 1.2.3 | 1.00 | 56.00 | 57.00 | OK | |
| r-release-macos-x86_64 | 1.2.3 | 3.00 | 127.00 | 130.00 | OK | |
| r-release-windows-x86_64 | 1.2.3 | 7.00 | 116.00 | 123.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.3 | ERROR | ||||
| r-oldrel-macos-x86_64 | 1.2.3 | 3.00 | 165.00 | 168.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.3 | 8.00 | 132.00 | 140.00 | OK |
Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown
2026-10-20 06:16:38.639 R[60363:243488] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
3: ar(x[, i], aic = TRUE)
4: spectrum0.ar(x)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: 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))})
9: try(spectrum0.ar(x)$spec)
10: safespec0(x[[i]][, j])
11: summary.mcmc.list(x)
12: summary(x)
13: mcmc2bugs(samples, model.file = model.file, program = "jags", DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin, checkMissing = checkMissing)
14: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15: eval(c.expr, envir = args, enclos = envir)
16: eval(c.expr, envir = args, enclos = envir)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
21: FUN(X[[i]], ...)
22: lapply(X = S, FUN = FUN, ...)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
26: 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))})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
Traceback:
1:
28: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) series = series, ...)
2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, 29: series = series, ...)FUN(X[[i]], ...)
3: 30: ar(x[, i], aic = TRUE)lapply(seq_len(cores), inner.do)
4:
spectrum0.ar(x)31:
5: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, doTryCatch(return(expr), name, parentenv, handler) mc.silent = silent, mc.cores = cores)
6:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: 7: tryCatchList(expr, classes, parentenv, handlers)e$fun(obj, substitute(ex), parent.frame(), e$data)
8: 33: tryCatch(expr, error = function(e) {foreach(i = 1:n.cluster) %dopar% { call <- conditionCall(e) jags(data = data, parameters.to.save = parameters.to.save, if (!is.null(call)) { model.file = model.file, n.chains = 1, n.iter = n.iter, if (identical(call[[1L]], quote(doTryCatch))) n.burnin = n.burnin, n.thin = n.thin) call <- sys.call(-4L)} dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")34: LONG <- 75Ljags.parallel(data = d, parameters.to.save = p, model.file = tmf, sm <- strsplit(conditionMessage(e), "\n")[[1L]] n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") n.thin = n.thin) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 35: type = "b")mixSource(obs, sources, slope, ngens = 20000, ncores = 2) if (w > LONG)
prefix <- paste0(prefix, "\n ")36: }eval(expr, envir) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")37: .Internal(seterrmessage(msg[1L]))eval(expr, envir) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)38: .Internal(printDeferredWarnings())withVisible(eval(expr, envir)) }
invisible(structure(msg, class = "try-error", condition = e))39: })withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) { 9: try(spectrum0.ar(x)$spec) watcher$capture_plot_and_output()
if (on_message$capture) {10: watcher$push(cnd)safespec0(x[[i]][, j]) } if (on_message$silence) {
invokeRestart("muffleMessage")11: }summary.mcmc.list(x)}, warning = function (cnd)
{12: if (getOption("warn") >= 2 || getOption("warn") < 0) {summary(x) return()
13: }mcmc2bugs(samples, model.file = model.file, program = "jags", watcher$capture_plot_and_output() DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, if (on_warning$capture) { n.thin = n.thin, checkMissing = checkMissing) cnd <- sanitize_call(cnd)
watcher$push(cnd)14: }jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, if (on_warning$silence) { n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin) invokeRestart("muffleWarning")
}15: }, error = function (cnd) eval(c.expr, envir = args, enclos = envir){
watcher$capture_plot_and_output()16: cnd <- sanitize_call(cnd)eval(c.expr, envir = args, enclos = envir) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"),
17: stop = invokeRestart("eval_stop"), error = NULL)doTryCatch(return(expr), name, parentenv, handler)})
18: 40: tryCatchOne(expr, names, parentenv, handlers[[1L]])eval(call)
19: 41: tryCatchList(expr, classes, parentenv, handlers)eval(call)
42: 20: with_handlers({tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))21: watcher$capture_plot_and_output()FUN(X[[i]], ...) watcher$print_value(ev$value, ev$visible, envir)
}22: TRUElapply(X = S, FUN = FUN, ...)}, handlers)
23: 43: doTryCatch(return(expr), name, parentenv, handler)doWithOneRestart(return(expr), restart)
24: 44: withOneRestart(expr, restarts[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: 25: withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
46: 26: doWithOneRestart(return(expr), restart)tryCatch(expr, error = function(e) {
call <- conditionCall(e)47: if (!is.null(call)) {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)48: dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")withRestartList(expr, restarts) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]49: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withRestarts(with_handlers({ if (is.na(w)) for (expr in tle$exprs) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ev <- withVisible(eval(expr, envir)) type = "b") watcher$capture_plot_and_output() if (w > LONG) watcher$print_value(ev$value, ev$visible, envir) prefix <- paste0(prefix, "\n ") } } TRUE else prefix <- "Error : "}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)50: .Internal(printDeferredWarnings())evaluate::evaluate(...) }
invisible(structure(msg, class = "try-error", condition = e))51: })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, 27: stop_on_error = if (is.numeric(options$error)) options$error else {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
if (options$error && options$include) 28: 0LsendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) else 2L
}, output_handler = knit_handlers(options$render, options))29: FUN(X[[i]], ...)
52: 30: in_dir(input_dir(), expr)lapply(seq_len(cores), inner.do)
53: 31: in_input_dir(evaluate(code, envir = env, new_device = FALSE, mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, mc.silent = silent, mc.cores = cores) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {32: if (options$error && options$include) e$fun(obj, substitute(ex), parent.frame(), e$data) 0L
else 2L33: }, output_handler = knit_handlers(options$render, options)))foreach(i = 1:n.cluster) %dopar% {
jags(data = data, parameters.to.save = parameters.to.save, 54: model.file = model.file, n.chains = 1, n.iter = n.iter, eng_r(options) n.burnin = n.burnin, n.thin = n.thin)
}55:
block_exec(params)34:
jags.parallel(data = d, parameters.to.save = p, model.file = tmf, 56: n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, call_block(x) n.thin = n.thin)
57: 35: process_group(group)mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
58: 36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), eval(expr, envir) error = function(e) {
if (progress && is.function(pb$interrupt)) 37: pb$interrupt()eval(expr, envir) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)38: })withVisible(eval(expr, envir))
59: 39: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), withCallingHandlers(code, error = function (e) error = function(e) {rlang::entrace(e), message = function (cnd) if (progress && is.function(pb$interrupt)) { pb$interrupt() watcher$capture_plot_and_output() if (is_R_CMD_build() || is_R_CMD_check()) if (on_message$capture) { error <<- format(e) watcher$push(cnd) }), list(rlang_trace_top_env = knit_global())) }
if (on_message$silence) {60: invokeRestart("muffleMessage")xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) {}, warning = function (cnd) if (progress && is.function(pb$interrupt)) { pb$interrupt() if (getOption("warn") >= 2 || getOption("warn") < 0) { if (is_R_CMD_build() || is_R_CMD_check()) return() error <<- format(e) } }), list(rlang_trace_top_env = knit_global())), function(loc) { watcher$capture_plot_and_output() setwd(wd) if (on_warning$capture) { write_utf8(res, output %n% stdout()) cnd <- sanitize_call(cnd) paste0("\nQuitting from ", loc, if (!is.null(error)) watcher$push(cnd) paste0("\n", rule(), error, "\n", rule())) }}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) if (on_warning$silence) {
invokeRestart("muffleWarning")61: }process_file(text, output)}, error = function (cnd)
{ watcher$capture_plot_and_output()62: cnd <- sanitize_call(cnd)knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 63: stop = invokeRestart("eval_stop"), error = NULL)rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }) output_dir = getwd(), ...)
40: 64: eval(call)vweave_rmarkdown(...)
41: 65: eval(call)engine$weave(file, quiet = quiet, encoding = enc)
42: 66: with_handlers({doTryCatch(return(expr), name, parentenv, handler) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))67: watcher$capture_plot_and_output()tryCatchOne(expr, names, parentenv, handlers[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
}68: TRUEtryCatchList(expr, classes, parentenv, handlers)}, handlers)
69: 43: tryCatch({doWithOneRestart(return(expr), restart) engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)44: output <- find_vignette_product(name, by = "weave", engine = engine)withOneRestart(expr, restarts[[1L]]) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)45: output <- find_vignette_product(name, by = "texi2pdf", withRestartList(expr, restarts[-nr]) engine = engine)
}46: outputs <- c(outputs, output)doWithOneRestart(return(expr), restart)}, error = function(e) {
thisOK <<- FALSE47: fails <<- c(fails, file)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))48: })withRestartList(expr, restarts)
70: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", 49: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpAAha2C/filed69c2cc15dad.rds")withRestarts(with_handlers({
for (expr in tle$exprs) {An irrecoverable exception occurred. R is aborting now ...
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)
50: evaluate::evaluate(...)
51: 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$render, options))
52: in_dir(input_dir(), expr)
53: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
54: eng_r(options)
55: block_exec(params)
56: call_block(x)
57: process_group(group)
58: 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) })
59: 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()))
60: 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)
61: process_file(text, output)
62: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
63: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
64: vweave_rmarkdown(...)
65: engine$weave(file, quiet = quiet, encoding = enc)
66: doTryCatch(return(expr), name, parentenv, handler)
67: tryCatchOne(expr, names, parentenv, handlers[[1L]])
68: tryCatchList(expr, classes, parentenv, handlers)
69: tryCatch({ engine$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)))})
70: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpAAha2C/filed69c2cc15dad.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from isoWater.Rmd:176-179 [mixSource1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `1:n.parameters`:
! argument of length 0
---
Backtrace:
▆
1. └─isoWater::mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
2. └─isoWater:::jags.parallel(...)
3. └─isoWater:::as.bugs.array2(...)
4. └─base::paste("P", 1:n.parameters, sep = "")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'isoWater.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘isoWater.Rmd’
SUMMARY: processing the following file failed:
‘isoWater.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64