Last updated on 2026-10-22 23:56:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 4.39 | 64.93 | 69.32 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.25 | 50.38 | 53.63 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 61.40 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 55.06 | OK | |||
| r-devel-windows-x86_64 | 1.2.3 | 7.00 | 753.00 | 760.00 | OK | |
| r-patched-linux-x86_64 | 1.2.3 | 4.48 | 60.02 | 64.50 | 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 | 2.00 | 82.00 | 84.00 | 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 | 140.00 | 148.00 | 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
2026-10-23 00:31:23.618 R[74217:261910] 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]))
Traceback:
1: if (!silent && isTRUE(getOption("show.error.messages"))) {ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, cat(msg, file = outFile) series = series, ...) .Internal(printDeferredWarnings())
} 2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...) invisible(structure(msg, class = "try-error", condition = e))
}) 3: ar(x[, i], aic = TRUE)
4: spectrum0.ar(x) 9:
5: try(spectrum0.ar(x)$spec)doTryCatch(return(expr), name, parentenv, handler)
6: 10: safespec0(x[[i]][, j])tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: 11: tryCatchList(expr, classes, parentenv, handlers)
summary.mcmc.list(x) 8: tryCatch(expr, error = function(e) {
call <- conditionCall(e)12: if (!is.null(call)) {summary(x) if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)
dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L13: sm <- strsplit(conditionMessage(e), "\n")[[1L]]mcmc2bugs(samples, model.file = model.file, program = "jags", w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, if (is.na(w)) n.thin = n.thin, checkMissing = checkMissing) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")14: if (w > LONG) jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, prefix <- paste0(prefix, "\n ") n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin) }
else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")15: .Internal(seterrmessage(msg[1L]))eval(c.expr, envir = args, enclos = envir) if (!silent && isTRUE(getOption("show.error.messages"))) {
16: cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))eval(c.expr, envir = args, enclos = envir)})
9: 17: doTryCatch(return(expr), name, parentenv, handler)try(spectrum0.ar(x)$spec)
10:
safespec0(x[[i]][, j])
18: 11: summary.mcmc.list(x)tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: summary(x)19:
tryCatchList(expr, classes, parentenv, handlers)13: mcmc2bugs(samples, model.file = model.file, program = "jags",
DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, 20: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) n.thin = n.thin, checkMissing = checkMissing)
14:
jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, 21: n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)FUN(X[[i]], ...)
22: 15: eval(c.expr, envir = args, enclos = envir)
lapply(X = S, FUN = FUN, ...)16:
eval(c.expr, envir = args, enclos = envir)
17: 23: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
24: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: 19: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
26: 20: tryCatch(expr, error = function(e) {tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) 21: call <- sys.call(-4L)FUN(X[[i]], ...) dcall <- deparse(call, nlines = 1L)
22: prefix <- paste("Error in", dcall, ": ")lapply(X = S, FUN = FUN, ...) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]23: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")doTryCatch(return(expr), name, parentenv, handler) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 24: type = "b")tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (w > LONG)
prefix <- paste0(prefix, "\n ") }25: else prefix <- "Error : "tryCatchList(expr, classes, parentenv, handlers) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {26: tryCatch(expr, error = function(e) { cat(msg, file = outFile) call <- conditionCall(e) if (!is.null(call)) { .Internal(printDeferredWarnings()) if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) invisible(structure(msg, class = "try-error", condition = e))}) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L27: sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (is.na(w))
28: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
type = "b")29: if (w > LONG) FUN(X[[i]], ...) prefix <- paste0(prefix, "\n ")
}30: lapply(seq_len(cores), inner.do) else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) {31: cat(msg, file = outFile)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, .Internal(printDeferredWarnings()) mc.silent = silent, mc.cores = cores)
}32: invisible(structure(msg, class = "try-error", condition = e))e$fun(obj, substitute(ex), parent.frame(), e$data)})
27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
33: foreach(i = 1:n.cluster) %dopar% {28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
jags(data = data, parameters.to.save = parameters.to.save, 29: model.file = model.file, n.chains = 1, n.iter = n.iter, FUN(X[[i]], ...)
n.burnin = n.burnin, n.thin = n.thin)30: lapply(seq_len(cores), inner.do)}
31: 34: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)jags.parallel(data = d, parameters.to.save = p, model.file = tmf,
n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, 32: n.thin = n.thin)e$fun(obj, substitute(ex), parent.frame(), e$data)
35: 33: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)foreach(i = 1:n.cluster) %dopar% {
jags(data = data, parameters.to.save = parameters.to.save, 36: eval(expr, envir) model.file = model.file, n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
}
34: 37: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, eval(expr, envir)
n.thin = n.thin)
35: 38: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)withVisible(eval(expr, envir))
36:
eval(expr, envir)39:
withCallingHandlers(code, error = function (e) 37: eval(expr, envir)
rlang::entrace(e), message = function (cnd) {38: watcher$capture_plot_and_output()withVisible(eval(expr, envir))
if (on_message$capture) {39: watcher$push(cnd)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) }{ if (on_message$silence) { watcher$capture_plot_and_output() if (on_message$capture) { invokeRestart("muffleMessage") } watcher$push(cnd)}, warning = function (cnd) { } if (getOption("warn") >= 2 || getOption("warn") < 0) { if (on_message$silence) { invokeRestart("muffleMessage") return() } }}, warning = function (cnd) watcher$capture_plot_and_output(){ if (on_warning$capture) { cnd <- sanitize_call(cnd) if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$push(cnd) } return() if (on_warning$silence) { } watcher$capture_plot_and_output() if (on_warning$capture) { invokeRestart("muffleWarning") } cnd <- sanitize_call(cnd) watcher$push(cnd)}, error = function (cnd) } if (on_warning$silence) { invokeRestart("muffleWarning"){ watcher$capture_plot_and_output() } cnd <- sanitize_call(cnd)}, error = function (cnd) watcher$push(cnd){ switch(on_error, continue = invokeRestart("eval_continue"), watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) stop = invokeRestart("eval_stop"), error = NULL) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), }) stop = invokeRestart("eval_stop"), error = NULL)
})
40: eval(call)
40: 41: eval(call)eval(call)
42: 41: eval(call)with_handlers({
42: for (expr in tle$exprs) {with_handlers({ ev <- withVisible(eval(expr, envir)) for (expr in tle$exprs) { watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) watcher$print_value(ev$value, ev$visible, envir) watcher$capture_plot_and_output() } watcher$print_value(ev$value, ev$visible, envir) TRUE}, handlers) } TRUE
43: doWithOneRestart(return(expr), restart)}, handlers)
44: 43: withOneRestart(expr, restarts[[1L]])
doWithOneRestart(return(expr), restart)45: withRestartList(expr, restarts[-nr])
46: doWithOneRestart(return(expr), restart)44: withOneRestart(expr, restarts[[1L]])
45: 47: withRestartList(expr, restarts[-nr])
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
46: 48: withRestartList(expr, restarts)
doWithOneRestart(return(expr), restart)49:
withRestarts(with_handlers({47: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)48: }withRestartList(expr, restarts) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
49: 50: withRestarts(with_handlers({evaluate::evaluate(...)
for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))51: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$capture_plot_and_output() keep_message = if (is.numeric(options$message)) TRUE else options$message, watcher$print_value(ev$value, ev$visible, envir) stop_on_error = if (is.numeric(options$error)) options$error else { } TRUE if (options$error && options$include) 0L else 2L}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) }, output_handler = knit_handlers(options$render, options))
52: 50: in_dir(input_dir(), expr)evaluate::evaluate(...)
53: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 51: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else { keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) if (options$error && options$include) 0L 0L else 2L else 2L }, output_handler = knit_handlers(options$render, options)) }, output_handler = knit_handlers(options$render, options)))
54: 52: eng_r(options)in_dir(input_dir(), expr)
55: block_exec(params)
56: 53: in_input_dir(evaluate(code, envir = env, new_device = FALSE, call_block(x) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
57: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {process_group(group) if (options$error && options$include)
58: 0LwithCallingHandlers(if (tangle) process_tangle(group) else process_group(group), else 2L error = function(e) { if (progress && is.function(pb$interrupt)) }, output_handler = knit_handlers(options$render, options))) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 54: error <<- format(e) })eng_r(options)
59: 55: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), block_exec(params) error = function(e) {
if (progress && is.function(pb$interrupt)) 56: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) call_block(x) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))57:
process_group(group)60:
58: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (progress && is.function(pb$interrupt)) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) pb$interrupt() }) if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {59: setwd(wd)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), write_utf8(res, output %n% stdout()) error = function(e) { if (progress && is.function(pb$interrupt)) paste0("\nQuitting from ", loc, if (!is.null(error)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
60: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 61: error = function(e) { if (progress && is.function(pb$interrupt)) process_file(text, output) pb$interrupt()
62: if (is_R_CMD_build() || is_R_CMD_check()) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 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)) 63: paste0("\n", rule(), error, "\n", rule()))rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) output_dir = getwd(), ...)
61:
process_file(text, output)64:
vweave_rmarkdown(...)62: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
63: 65: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
engine$weave(file, quiet = quiet, encoding = enc)64:
vweave_rmarkdown(...)
66: 65: doTryCatch(return(expr), name, parentenv, handler)engine$weave(file, quiet = quiet, encoding = enc)
67: 66: tryCatchOne(expr, names, parentenv, handlers[[1L]])
doTryCatch(return(expr), name, parentenv, handler)
68: 67: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
68:
69: tryCatchList(expr, classes, parentenv, handlers)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)
69: setwd(startdir)tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) texi2pdf(file = output, clean = FALSE, quiet = quiet) } output <- find_vignette_product(name, by = "texi2pdf", outputs <- c(outputs, output) engine = engine)}, error = function(e) { } thisOK <<- FALSE fails <<- c(fails, file) outputs <- c(outputs, output) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }, error = function(e) { file, conditionMessage(e))) thisOK <<- FALSE}) fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 70: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", file, conditionMessage(e)))}) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5E6Qel/fileec9c72e0982c.rds")
70: An irrecoverable exception occurred. R is aborting now ...
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp5E6Qel/fileec9c72e0982c.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