Last updated on 2026-10-24 12:51:36 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 3.39 | 65.58 | 68.97 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.78 | 51.18 | 54.96 | 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 | 124.00 | 131.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.3 | 2.00 | 83.00 | 85.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.2.3 | 3.00 | 165.00 | 168.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.3 | 9.00 | 138.00 | 147.00 | 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
2026-10-24 20:33:23.853 R[72337:260298] 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")
Traceback:
if (is.na(w)) 1: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, type = "b") series = series, ...) if (w > LONG)
prefix <- paste0(prefix, "\n ") } 2: else prefix <- "Error : "ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) series = series, ...) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile) 3: .Internal(printDeferredWarnings())ar(x[, i], aic = TRUE) }
invisible(structure(msg, class = "try-error", condition = e)) 4: })spectrum0.ar(x)
9: 5: try(spectrum0.ar(x)$spec)doTryCatch(return(expr), name, parentenv, handler)
10: 6: safespec0(x[[i]][, j])tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: 7: summary.mcmc.list(x)tryCatchList(expr, classes, parentenv, handlers)
12: 8: summary(x)tryCatch(expr, error = function(e) {
call <- conditionCall(e)13: if (!is.null(call)) {mcmc2bugs(samples, model.file = model.file, program = "jags", if (identical(call[[1L]], quote(doTryCatch))) DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, call <- sys.call(-4L) n.thin = n.thin, checkMissing = checkMissing) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")14: LONG <- 75Ljags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, sm <- strsplit(conditionMessage(e), "\n")[[1L]] n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
15: if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], eval(c.expr, envir = args, enclos = envir)
type = "b")16: if (w > LONG) eval(c.expr, envir = args, enclos = envir) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : "17: msg <- paste0(prefix, conditionMessage(e), "\n")doTryCatch(return(expr), name, parentenv, handler) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {18: cat(msg, file = outFile)tryCatchOne(expr, names, parentenv, handlers[[1L]]) .Internal(printDeferredWarnings())
}19: invisible(structure(msg, class = "try-error", condition = e))tryCatchList(expr, classes, parentenv, handlers)})
9: 20: try(spectrum0.ar(x)$spec)tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
10: 21: safespec0(x[[i]][, j])FUN(X[[i]], ...)
11: summary.mcmc.list(x)
22: 12: summary(x)lapply(X = S, FUN = FUN, ...)
23: 13: mcmc2bugs(samples, model.file = model.file, program = "jags", doTryCatch(return(expr), name, parentenv, handler)
24: DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin, checkMissing = checkMissing)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: 25: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, tryCatchList(expr, classes, parentenv, handlers) n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15:
eval(c.expr, envir = args, enclos = envir)26:
tryCatch(expr, error = function(e) {16: call <- conditionCall(e)eval(c.expr, envir = args, enclos = envir) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L)17: dcall <- deparse(call, nlines = 1L)doTryCatch(return(expr), name, parentenv, handler)
prefix <- paste("Error in", dcall, ": ")18: LONG <- 75LtryCatchOne(expr, names, parentenv, handlers[[1L]]) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")19: if (is.na(w)) tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) 20: prefix <- paste0(prefix, "\n ")tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) }
else prefix <- "Error : "21: msg <- paste0(prefix, conditionMessage(e), "\n")FUN(X[[i]], ...) .Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {22: cat(msg, file = outFile)lapply(X = S, FUN = FUN, ...) .Internal(printDeferredWarnings())
}23: invisible(structure(msg, class = "try-error", condition = e))doTryCatch(return(expr), name, parentenv, handler)})
24: 27: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: 25: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))tryCatchList(expr, classes, parentenv, handlers)
29: 26: FUN(X[[i]], ...)tryCatch(expr, error = function(e) {
call <- conditionCall(e)30: if (!is.null(call)) {lapply(seq_len(cores), inner.do) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)31: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, dcall <- deparse(call, nlines = 1L) mc.silent = silent, mc.cores = cores) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L32: sm <- strsplit(conditionMessage(e), "\n")[[1L]]e$fun(obj, substitute(ex), parent.frame(), e$data) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 33: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], foreach(i = 1:n.cluster) %dopar% { type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } jags(data = data, parameters.to.save = parameters.to.save, else prefix <- "Error : " model.file = model.file, n.chains = 1, n.iter = n.iter, msg <- paste0(prefix, conditionMessage(e), "\n") n.burnin = n.burnin, n.thin = n.thin) .Internal(seterrmessage(msg[1L]))} if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)34: .Internal(printDeferredWarnings())jags.parallel(data = d, parameters.to.save = p, model.file = tmf, } n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, invisible(structure(msg, class = "try-error", condition = e)) n.thin = n.thin)})
35: 27: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
36: 28: eval(expr, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
37: 29: eval(expr, envir)FUN(X[[i]], ...)
38:
withVisible(eval(expr, envir))30:
lapply(seq_len(cores), inner.do)39:
withCallingHandlers(code, error = function (e) 31: rlang::entrace(e), message = function (cnd) mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, { mc.silent = silent, mc.cores = cores) watcher$capture_plot_and_output()
32: if (on_message$capture) {e$fun(obj, substitute(ex), parent.frame(), e$data) watcher$push(cnd)
}33: if (on_message$silence) {foreach(i = 1:n.cluster) %dopar% { invokeRestart("muffleMessage") jags(data = data, parameters.to.save = parameters.to.save, } model.file = model.file, n.chains = 1, n.iter = n.iter, }, warning = function (cnd) n.burnin = n.burnin, n.thin = n.thin){} if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()34: }jags.parallel(data = d, parameters.to.save = p, model.file = tmf, watcher$capture_plot_and_output() if (on_warning$capture) { n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, cnd <- sanitize_call(cnd) watcher$push(cnd) n.thin = n.thin) }
if (on_warning$silence) {35: invokeRestart("muffleWarning")mixSource(obs, sources, slope, ngens = 20000, ncores = 2) }
}, error = function (cnd) 36: {eval(expr, envir) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)37: watcher$push(cnd)eval(expr, envir) switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL)})38:
withVisible(eval(expr, envir))40:
eval(call)39:
withCallingHandlers(code, error = function (e) 41: rlang::entrace(e), message = function (cnd) eval(call){
watcher$capture_plot_and_output()42: if (on_message$capture) {with_handlers({ watcher$push(cnd) for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir)) if (on_message$silence) { watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) invokeRestart("muffleMessage") } } TRUE}, warning = function (cnd) }, handlers)
{43: if (getOption("warn") >= 2 || getOption("warn") < 0) {doWithOneRestart(return(expr), restart) return()
}44: watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]]) if (on_warning$capture) {
cnd <- sanitize_call(cnd)45: watcher$push(cnd)withRestartList(expr, restarts[-nr]) } if (on_warning$silence) {
invokeRestart("muffleWarning")46: }doWithOneRestart(return(expr), restart)}, error = function (cnd)
{47: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
48: cnd <- sanitize_call(cnd)withRestartList(expr, restarts) watcher$push(cnd)
49: withRestarts(with_handlers({ for (expr in tle$exprs) { switch(on_error, continue = invokeRestart("eval_continue"), ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() stop = invokeRestart("eval_stop"), error = NULL) watcher$print_value(ev$value, ev$visible, envir)}) }
TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)40:
eval(call)50:
evaluate::evaluate(...)41:
eval(call)51:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 42: keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {with_handlers({ if (options$error && options$include) 0L for (expr in tle$exprs) { else 2L }, output_handler = knit_handlers(options$render, options)) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()52: watcher$print_value(ev$value, ev$visible, envir)in_dir(input_dir(), expr) }
TRUE53: }, handlers)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 43: keep_message = if (is.numeric(options$message)) TRUE else options$message, doWithOneRestart(return(expr), restart) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 44: 0LwithOneRestart(expr, restarts[[1L]]) else 2L }, output_handler = knit_handlers(options$render, options)))
45: 54: eng_r(options)withRestartList(expr, restarts[-nr])
55: 46: block_exec(params)
doWithOneRestart(return(expr), restart)56:
call_block(x)47:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])57:
process_group(group)48:
withRestartList(expr, restarts)58:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 49: error = function(e) { if (progress && is.function(pb$interrupt)) withRestarts(with_handlers({ pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() }) watcher$print_value(ev$value, ev$visible, envir)
}59: TRUEwith_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) error = function(e) {
if (progress && is.function(pb$interrupt)) pb$interrupt()50: if (is_R_CMD_build() || is_R_CMD_check()) evaluate::evaluate(...) error <<- format(e)
}), list(rlang_trace_top_env = knit_global()))51:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 60: keep_message = if (is.numeric(options$message)) TRUE else options$message, xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), stop_on_error = if (is.numeric(options$error)) options$error else { error = function(e) { if (options$error && options$include) if (progress && is.function(pb$interrupt)) 0L pb$interrupt() else 2L if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }, output_handler = knit_handlers(options$render, options)) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)52: write_utf8(res, output %n% stdout())in_dir(input_dir(), expr) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)53:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 61: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, process_file(text, output) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {62: if (options$error && options$include) knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 0L
63: else 2Lrmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), }, output_handler = knit_handlers(options$render, options))) output_dir = getwd(), ...)
54: 64: eng_r(options)vweave_rmarkdown(...)
65: 55: engine$weave(file, quiet = quiet, encoding = enc)block_exec(params)
66: 56: doTryCatch(return(expr), name, parentenv, handler)call_block(x)
67:
tryCatchOne(expr, names, parentenv, handlers[[1L]])57:
process_group(group)68:
tryCatchList(expr, classes, parentenv, handlers)58:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 69: error = function(e) {tryCatch({ if (progress && is.function(pb$interrupt)) engine$weave(file, quiet = quiet, encoding = enc) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) setwd(startdir) error <<- format(e) output <- find_vignette_product(name, by = "weave", engine = engine) }) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)59: output <- find_vignette_product(name, by = "texi2pdf", engine = engine)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } error = function(e) { outputs <- c(outputs, output) if (progress && is.function(pb$interrupt)) }, error = function(e) { pb$interrupt() thisOK <<- FALSE if (is_R_CMD_build() || is_R_CMD_check()) fails <<- c(fails, file) error <<- format(e) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", }), list(rlang_trace_top_env = knit_global())) file, conditionMessage(e)))
})60:
70: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp6ah9V3/fileddbd584fc8a6.rds") error = function(e) {
if (progress && is.function(pb$interrupt)) An irrecoverable exception occurred. R is aborting now ...
pb$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/Rtmp6ah9V3/fileddbd584fc8a6.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