Last updated on 2026-11-03 10:54:46 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 3.96 | 65.56 | 69.52 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.31 | 51.25 | 54.56 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 51.01 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 52.65 | OK | |||
| r-devel-windows-x86_64 | 1.2.3 | 6.00 | 126.00 | 132.00 | OK | |
| r-patched-linux-x86_64 | 1.2.3 | 4.47 | 60.70 | 65.17 | OK | |
| r-release-linux-x86_64 | 1.2.3 | 4.03 | 59.92 | 63.95 | 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 | 6.00 | 115.00 | 121.00 | 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 | 135.00 | 143.00 | 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
2026-11-03 14:46:28.063 R[23978:389047] 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)
Traceback:
1: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, 6: series = series, ...)tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: 2: tryCatchList(expr, classes, parentenv, handlers)ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
3:
ar(x[, i], aic = TRUE) 8:
4: spectrum0.ar(x)tryCatch(expr, error = function(e) {
call <- conditionCall(e) 5: if (!is.null(call)) {doTryCatch(return(expr), name, parentenv, handler) if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L) 6: dcall <- deparse(call, nlines = 1L)tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste("Error in", dcall, ": ")
LONG <- 75L 7: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w)) 8: w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], tryCatch(expr, error = function(e) { type = "b") call <- conditionCall(e) if (w > LONG) if (!is.null(call)) { prefix <- paste0(prefix, "\n ") if (identical(call[[1L]], quote(doTryCatch))) } call <- sys.call(-4L) else prefix <- "Error : " dcall <- deparse(call, nlines = 1L) msg <- paste0(prefix, conditionMessage(e), "\n") prefix <- paste("Error in", dcall, ": ") .Internal(seterrmessage(msg[1L])) LONG <- 75L if (!silent && isTRUE(getOption("show.error.messages"))) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] cat(msg, file = outFile) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") .Internal(printDeferredWarnings()) if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invisible(structure(msg, class = "try-error", condition = e)) type = "b")}) if (w > LONG)
prefix <- paste0(prefix, "\n ") 9: }try(spectrum0.ar(x)$spec) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")10: .Internal(seterrmessage(msg[1L]))safespec0(x[[i]][, j]) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile)
.Internal(printDeferredWarnings())11: }summary.mcmc.list(x) invisible(structure(msg, class = "try-error", condition = e))
})12:
summary(x) 9:
13: try(spectrum0.ar(x)$spec)mcmc2bugs(samples, model.file = model.file, program = "jags",
DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, 10: n.thin = n.thin, checkMissing = checkMissing)safespec0(x[[i]][, j])
11: summary.mcmc.list(x)
12: 14: summary(x)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)13:
mcmc2bugs(samples, model.file = model.file, program = "jags", 15: DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, eval(c.expr, envir = args, enclos = envir) n.thin = n.thin, checkMissing = checkMissing)
14: 16: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, eval(c.expr, envir = args, enclos = envir) n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
17: 15: doTryCatch(return(expr), name, parentenv, handler)eval(c.expr, envir = args, enclos = envir)
18: 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
eval(c.expr, envir = args, enclos = envir)19:
tryCatchList(expr, classes, parentenv, handlers)17:
doTryCatch(return(expr), name, parentenv, handler)20:
tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)18:
tryCatchOne(expr, names, parentenv, handlers[[1L]])21:
FUN(X[[i]], ...)19:
tryCatchList(expr, classes, parentenv, handlers)22:
lapply(X = S, FUN = FUN, ...)20:
tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)23:
doTryCatch(return(expr), name, parentenv, handler)21:
FUN(X[[i]], ...)24:
tryCatchOne(expr, names, parentenv, handlers[[1L]])22:
lapply(X = S, FUN = FUN, ...)25:
tryCatchList(expr, classes, parentenv, handlers)23:
doTryCatch(return(expr), name, parentenv, handler)26:
tryCatch(expr, error = function(e) {24: call <- conditionCall(e)tryCatchOne(expr, names, parentenv, handlers[[1L]]) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 25: call <- sys.call(-4L)tryCatchList(expr, classes, parentenv, handlers) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")26: LONG <- 75LtryCatch(expr, error = function(e) { sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- conditionCall(e) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (!is.null(call)) { if (is.na(w)) if (identical(call[[1L]], quote(doTryCatch))) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], call <- sys.call(-4L) type = "b") dcall <- deparse(call, nlines = 1L) if (w > LONG) prefix <- paste("Error in", dcall, ": ") prefix <- paste0(prefix, "\n ") LONG <- 75L } sm <- strsplit(conditionMessage(e), "\n")[[1L]] else prefix <- "Error : " w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") msg <- paste0(prefix, conditionMessage(e), "\n") if (is.na(w)) .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], cat(msg, file = outFile) type = "b") .Internal(printDeferredWarnings()) if (w > LONG) } prefix <- paste0(prefix, "\n ") invisible(structure(msg, class = "try-error", condition = e)) }}) else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")27: .Internal(seterrmessage(msg[1L]))try(lapply(X = S, FUN = FUN, ...), silent = TRUE) if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)28: .Internal(printDeferredWarnings())sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
invisible(structure(msg, class = "try-error", condition = e))29: })FUN(X[[i]], ...)
27: 30: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)lapply(seq_len(cores), inner.do)
28: 31: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)29:
FUN(X[[i]], ...)32:
e$fun(obj, substitute(ex), parent.frame(), e$data)30:
lapply(seq_len(cores), inner.do)33:
foreach(i = 1:n.cluster) %dopar% {31: jags(data = data, parameters.to.save = parameters.to.save, mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, model.file = model.file, n.chains = 1, n.iter = n.iter, mc.silent = silent, mc.cores = cores) n.burnin = n.burnin, n.thin = n.thin)
}32:
e$fun(obj, substitute(ex), parent.frame(), e$data)34:
jags.parallel(data = d, parameters.to.save = p, model.file = tmf, 33: n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, foreach(i = 1:n.cluster) %dopar% { n.thin = n.thin) jags(data = data, parameters.to.save = parameters.to.save,
model.file = model.file, n.chains = 1, n.iter = n.iter, 35: n.burnin = n.burnin, n.thin = n.thin)mixSource(obs, sources, slope, ngens = 20000, ncores = 2)}
36: 34: eval(expr, envir)jags.parallel(data = d, parameters.to.save = p, model.file = tmf,
n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, 37: n.thin = n.thin)eval(expr, envir)
35: 38: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)withVisible(eval(expr, envir))
39: 36: withCallingHandlers(code, error = function (e) eval(expr, envir)rlang::entrace(e), message = function (cnd)
{37: watcher$capture_plot_and_output()eval(expr, envir) if (on_message$capture) {
watcher$push(cnd)38: }withVisible(eval(expr, envir)) if (on_message$silence) {
invokeRestart("muffleMessage")39: }withCallingHandlers(code, error = function (e) }, warning = function (cnd) rlang::entrace(e), message = function (cnd) {{ if (getOption("warn") >= 2 || getOption("warn") < 0) { watcher$capture_plot_and_output() return() if (on_message$capture) { } watcher$push(cnd) watcher$capture_plot_and_output() } if (on_warning$capture) { if (on_message$silence) { cnd <- sanitize_call(cnd) invokeRestart("muffleMessage") watcher$push(cnd) } }}, warning = function (cnd) if (on_warning$silence) {{ invokeRestart("muffleWarning") if (getOption("warn") >= 2 || getOption("warn") < 0) { } return()}, error = function (cnd) }{ watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) if (on_warning$silence) {}) invokeRestart("muffleWarning")
}40: }, error = function (cnd) eval(call){
watcher$capture_plot_and_output()41: cnd <- sanitize_call(cnd)eval(call) watcher$push(cnd)
switch(on_error, continue = invokeRestart("eval_continue"), 42: stop = invokeRestart("eval_stop"), error = NULL)with_handlers({}) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))40: watcher$capture_plot_and_output()eval(call) watcher$print_value(ev$value, ev$visible, envir)
}41: TRUEeval(call)}, handlers)
42: 43: with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))44: watcher$capture_plot_and_output()withOneRestart(expr, restarts[[1L]]) watcher$print_value(ev$value, ev$visible, envir)
}45: TRUEwithRestartList(expr, restarts[-nr])}, handlers)
46: 43: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
47: 44: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withOneRestart(expr, restarts[[1L]])
48: 45: withRestartList(expr, restarts)withRestartList(expr, restarts[-nr])
49: 46: withRestarts(with_handlers({doWithOneRestart(return(expr), restart) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))47: watcher$capture_plot_and_output()withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) watcher$print_value(ev$value, ev$visible, envir)
}48: TRUEwithRestartList(expr, restarts)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
49: 50: withRestarts(with_handlers({evaluate::evaluate(...) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))51: watcher$capture_plot_and_output()evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, watcher$print_value(ev$value, ev$visible, envir) keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else { TRUE if (options$error && options$include) }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
0L50: else 2Levaluate::evaluate(...) }, output_handler = knit_handlers(options$render, options))
51: 52: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, in_dir(input_dir(), expr) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 53: 0Lin_input_dir(evaluate(code, envir = env, new_device = FALSE, else 2L keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, output_handler = knit_handlers(options$render, options)) keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {52: if (options$error && options$include) in_dir(input_dir(), expr) 0L
else 2L53: }, output_handler = knit_handlers(options$render, options)))in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 54: keep_message = if (is.numeric(options$message)) TRUE else options$message, eng_r(options) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 55: 0Lblock_exec(params) else 2L
}, output_handler = knit_handlers(options$render, options)))56:
call_block(x)54:
eng_r(options)57:
process_group(group)55:
block_exec(params)58:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 56: error = function(e) {call_block(x) if (progress && is.function(pb$interrupt))
pb$interrupt()57: if (is_R_CMD_build() || is_R_CMD_check()) process_group(group) error <<- format(e)
})58:
withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 59: error = function(e) {with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (progress && is.function(pb$interrupt)) error = function(e) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) error <<- format(e) pb$interrupt() }) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)59: }), list(rlang_trace_top_env = knit_global()))with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {60: if (progress && is.function(pb$interrupt)) xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() error = function(e) { if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) error <<- format(e) pb$interrupt() }), list(rlang_trace_top_env = knit_global())) if (is_R_CMD_build() || is_R_CMD_check())
error <<- format(e)60: }), list(rlang_trace_top_env = knit_global())), function(loc) {xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), setwd(wd) error = function(e) { write_utf8(res, output %n% stdout()) if (progress && is.function(pb$interrupt)) paste0("\nQuitting from ", loc, if (!is.null(error)) pb$interrupt() paste0("\n", rule(), error, "\n", rule())) if (is_R_CMD_build() || is_R_CMD_check()) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {61: setwd(wd)process_file(text, output) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 62: paste0("\n", rule(), error, "\n", rule()))knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
63: 61: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), process_file(text, output)
output_dir = getwd(), ...)62:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)64:
vweave_rmarkdown(...)63:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 65: output_dir = getwd(), ...)engine$weave(file, quiet = quiet, encoding = enc)
64: 66: vweave_rmarkdown(...)doTryCatch(return(expr), name, parentenv, handler)
65: 67: engine$weave(file, quiet = quiet, encoding = enc)tryCatchOne(expr, names, parentenv, handlers[[1L]])
66: 68: doTryCatch(return(expr), name, parentenv, handler)tryCatchList(expr, classes, parentenv, handlers)
67: 69: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)68: setwd(startdir)tryCatchList(expr, classes, parentenv, handlers) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {69: texi2pdf(file = output, clean = FALSE, quiet = quiet)tryCatch({ output <- find_vignette_product(name, by = "texi2pdf", engine$weave(file, quiet = quiet, encoding = enc) engine = engine) setwd(startdir) } output <- find_vignette_product(name, by = "weave", engine = engine) outputs <- c(outputs, output) if (!have.makefile && vignette_is_tex(output)) {}, error = function(e) { texi2pdf(file = output, clean = FALSE, quiet = quiet) thisOK <<- FALSE output <- find_vignette_product(name, by = "texi2pdf", fails <<- c(fails, file) engine = engine) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", } file, conditionMessage(e))) outputs <- c(outputs, output)})}, error = function(e) {
thisOK <<- FALSE70: fails <<- c(fails, file)tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpjDv49R/file292d330ac3fc.rds") file, conditionMessage(e)))
})An irrecoverable exception occurred. R is aborting now ...
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/RtmpjDv49R/file292d330ac3fc.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