Last updated on 2026-11-15 07:50:49 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 0.32 | 3.28 | 3.60 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.17 | 49.98 | 53.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 47.04 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 56.61 | OK | |||
| r-devel-windows-x86_64 | 1.2.3 | 7.00 | 130.00 | 137.00 | OK | |
| r-patched-linux-x86_64 | 1.2.3 | 0.32 | 2.19 | 2.51 | ERROR | |
| r-release-linux-x86_64 | 1.2.3 | 3.79 | 59.27 | 63.06 | 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 | 128.00 | 134.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.3 | 2.00 | 73.00 | 75.00 | 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 | 146.00 | 154.00 | OK |
Version: 1.2.3
Check: package dependencies
Result: ERROR
Package required but not available: 'R2jags'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown
2026-11-15 14:23:53.757 R[87085:286690] 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)
Traceback:
26: tryCatch(expr, error = function(e) { 1: call <- conditionCall(e)ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, if (!is.null(call)) { series = series, ...) if (identical(call[[1L]], quote(doTryCatch)))
2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
3: call <- sys.call(-4L)ar(x[, i], aic = TRUE) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") 4: LONG <- 75Lspectrum0.ar(x) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") 5: if (is.na(w)) doTryCatch(return(expr), name, parentenv, handler) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") 6: if (w > LONG) tryCatchOne(expr, names, parentenv, handlers[[1L]]) prefix <- paste0(prefix, "\n ")
} 7: else prefix <- "Error : "tryCatchList(expr, classes, parentenv, handlers) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) 8: if (!silent && isTRUE(getOption("show.error.messages"))) {tryCatch(expr, error = function(e) { cat(msg, file = outFile) call <- conditionCall(e) .Internal(printDeferredWarnings()) if (!is.null(call)) { } if (identical(call[[1L]], quote(doTryCatch))) invisible(structure(msg, class = "try-error", condition = e)) call <- sys.call(-4L)}) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")27: LONG <- 75Ltry(lapply(X = S, FUN = FUN, ...), silent = TRUE) sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")28: if (is.na(w)) sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")29: if (w > LONG) FUN(X[[i]], ...) prefix <- paste0(prefix, "\n ")
}30: else prefix <- "Error : "lapply(seq_len(cores), inner.do) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))31: if (!silent && isTRUE(getOption("show.error.messages"))) {mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, cat(msg, file = outFile) mc.silent = silent, mc.cores = cores) .Internal(printDeferredWarnings())
}32: invisible(structure(msg, class = "try-error", condition = e))e$fun(obj, substitute(ex), parent.frame(), e$data)})
33: 9: foreach(i = 1:n.cluster) %dopar% {try(spectrum0.ar(x)$spec)
jags(data = data, parameters.to.save = parameters.to.save, 10: model.file = model.file, n.chains = 1, n.iter = n.iter, safespec0(x[[i]][, j]) n.burnin = n.burnin, n.thin = n.thin)
}11:
summary.mcmc.list(x)
34: 12: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, summary(x) n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin,
n.thin = n.thin)13:
mcmc2bugs(samples, model.file = model.file, program = "jags", 35: mixSource(obs, sources, slope, ngens = 20000, ncores = 2) DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin,
n.thin = n.thin, checkMissing = checkMissing)36:
eval(expr, envir)14:
jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, 37: n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)eval(expr, envir)
15: 38: eval(c.expr, envir = args, enclos = envir)withVisible(eval(expr, envir))
16: 39: eval(c.expr, envir = args, enclos = envir)withCallingHandlers(code, error = function (e)
rlang::entrace(e), message = function (cnd) 17: {doTryCatch(return(expr), name, parentenv, handler) watcher$capture_plot_and_output()
if (on_message$capture) {18: watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) }
if (on_message$silence) {19: invokeRestart("muffleMessage")tryCatchList(expr, classes, parentenv, handlers) }
}, warning = function (cnd) 20: {tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()21: }FUN(X[[i]], ...) watcher$capture_plot_and_output()
if (on_warning$capture) {22: cnd <- sanitize_call(cnd)lapply(X = S, FUN = FUN, ...) watcher$push(cnd)
}23: doTryCatch(return(expr), name, parentenv, handler) if (on_warning$silence) {
invokeRestart("muffleWarning")24: }tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers)
}, error = function (cnd) 26: {tryCatch(expr, error = function(e) { call <- conditionCall(e) watcher$capture_plot_and_output() if (!is.null(call)) { cnd <- sanitize_call(cnd) if (identical(call[[1L]], quote(doTryCatch))) watcher$push(cnd) call <- sys.call(-4L) switch(on_error, continue = invokeRestart("eval_continue"), dcall <- deparse(call, nlines = 1L) stop = invokeRestart("eval_stop"), error = NULL) prefix <- paste("Error in", dcall, ": ")}) LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]40: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")eval(call) if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 41: type = "b")eval(call) if (w > LONG)
prefix <- paste0(prefix, "\n ")42: }with_handlers({ else prefix <- "Error : " for (expr in tle$exprs) { msg <- paste0(prefix, conditionMessage(e), "\n") ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() .Internal(seterrmessage(msg[1L])) watcher$print_value(ev$value, ev$visible, envir) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) TRUE .Internal(printDeferredWarnings())}, handlers) }
invisible(structure(msg, class = "try-error", condition = e))43: })doWithOneRestart(return(expr), restart)
27: 44: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)withOneRestart(expr, restarts[[1L]])
28: 45: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))withRestartList(expr, restarts[-nr])
29: 46: FUN(X[[i]], ...)doWithOneRestart(return(expr), restart)
30: 47: lapply(seq_len(cores), inner.do)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
31: 48: withRestartList(expr, restarts)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)49:
withRestarts(with_handlers({32: for (expr in tle$exprs) {e$fun(obj, substitute(ex), parent.frame(), e$data) ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)33: }foreach(i = 1:n.cluster) %dopar% { TRUE jags(data = data, parameters.to.save = parameters.to.save, }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) model.file = model.file, n.chains = 1, n.iter = n.iter,
n.burnin = n.burnin, n.thin = n.thin)50: }evaluate::evaluate(...)
51: 34: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, jags.parallel(data = d, parameters.to.save = p, model.file = tmf, keep_message = if (is.numeric(options$message)) TRUE else options$message, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, stop_on_error = if (is.numeric(options$error)) options$error else { n.thin = n.thin) if (options$error && options$include)
0L35: else 2LmixSource(obs, sources, slope, ngens = 20000, ncores = 2) }, output_handler = knit_handlers(options$render, options))
36: 52: eval(expr, envir)in_dir(input_dir(), expr)
37: 53: eval(expr, envir)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 38: keep_message = if (is.numeric(options$message)) TRUE else options$message, withVisible(eval(expr, envir)) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 39: 0LwithCallingHandlers(code, error = function (e) else 2Lrlang::entrace(e), message = function (cnd) }, output_handler = knit_handlers(options$render, options))){
watcher$capture_plot_and_output()54: eng_r(options) if (on_message$capture) {
watcher$push(cnd)55: }block_exec(params) if (on_message$silence) {
invokeRestart("muffleMessage")56: }call_block(x)}, warning = function (cnd)
{57: if (getOption("warn") >= 2 || getOption("warn") < 0) {process_group(group) return()
58: }withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), watcher$capture_plot_and_output() error = function(e) { if (on_warning$capture) { if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) } error <<- format(e) if (on_warning$silence) { }) invokeRestart("muffleWarning")
}59: }, error = function (cnd) with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), { error = function(e) { watcher$capture_plot_and_output() if (progress && is.function(pb$interrupt)) cnd <- sanitize_call(cnd) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) watcher$push(cnd) error <<- format(e) switch(on_error, continue = invokeRestart("eval_continue"), }), list(rlang_trace_top_env = knit_global())) stop = invokeRestart("eval_stop"), error = NULL)
})60:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 40: error = function(e) {eval(call) if (progress && is.function(pb$interrupt))
pb$interrupt()41: if (is_R_CMD_build() || is_R_CMD_check()) eval(call) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {42: setwd(wd)with_handlers({ write_utf8(res, output %n% stdout()) for (expr in tle$exprs) { paste0("\nQuitting from ", loc, if (!is.null(error)) ev <- withVisible(eval(expr, envir)) paste0("\n", rule(), error, "\n", rule())) watcher$capture_plot_and_output()}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) watcher$print_value(ev$value, ev$visible, envir)
}61: process_file(text, output) TRUE
}, handlers)62:
knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)43:
doWithOneRestart(return(expr), restart)63:
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withOneRestart(expr, restarts[[1L]])
output_dir = getwd(), ...)45:
withRestartList(expr, restarts[-nr])
64: vweave_rmarkdown(...)46:
65: doWithOneRestart(return(expr), restart)engine$weave(file, quiet = quiet, encoding = enc)
47: 66: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])doTryCatch(return(expr), name, parentenv, handler)
48: 67: withRestartList(expr, restarts)tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: 68: withRestarts(with_handlers({tryCatchList(expr, classes, parentenv, handlers) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))69: watcher$capture_plot_and_output()tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir) setwd(startdir) } output <- find_vignette_product(name, by = "weave", engine = engine) TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)50: output <- find_vignette_product(name, by = "texi2pdf", evaluate::evaluate(...) engine = engine)
}51: outputs <- c(outputs, output)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, }, error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, thisOK <<- FALSE stop_on_error = if (is.numeric(options$error)) options$error else { fails <<- c(fails, file) if (options$error && options$include) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 0L file, conditionMessage(e))) else 2L}) }, output_handler = knit_handlers(options$render, options))
70: 52: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", in_dir(input_dir(), expr) skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpCAnwa0/file109901de8edb0.rds")
53:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, An irrecoverable exception occurred. R is aborting now ...
keep_warning = if (is.numeric(options$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/RtmpCAnwa0/file109901de8edb0.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