Last updated on 2026-08-03 01:49:26 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.2 | 3.89 | 63.68 | 67.57 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.2 | 3.44 | 49.65 | 53.09 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.2.2 | 8.00 | 109.55 | 117.55 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.2 | 49.61 | OK | |||
| r-devel-windows-x86_64 | 1.2.2 | 7.00 | 112.00 | 119.00 | OK | |
| r-patched-linux-x86_64 | 1.2.2 | 4.34 | 59.72 | 64.06 | OK | |
| r-release-linux-x86_64 | 1.2.2 | 4.31 | 59.81 | 64.12 | OK | |
| r-release-macos-arm64 | 1.2.2 | 1.00 | 65.00 | 66.00 | OK | |
| r-release-macos-x86_64 | 1.2.2 | 3.00 | 116.00 | 119.00 | OK | |
| r-release-windows-x86_64 | 1.2.2 | 7.00 | 120.00 | 127.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.2 | 1.00 | 58.00 | 59.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.2.2 | 3.00 | 120.00 | 123.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.2 | 9.00 | 131.00 | 140.00 | OK |
Version: 1.2.2
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp1KOkHh’ ‘~/tmp/scratch/Rtmp1YdRZL’
‘~/tmp/scratch/Rtmp2R301Z’ ‘~/tmp/scratch/Rtmp2hZR0x’
‘~/tmp/scratch/Rtmp2pVdrq’ ‘~/tmp/scratch/Rtmp32nE2R’
‘~/tmp/scratch/Rtmp3aNbEl’ ‘~/tmp/scratch/Rtmp41brrX’
‘~/tmp/scratch/Rtmp4390sS’ ‘~/tmp/scratch/Rtmp5ZP59g’
‘~/tmp/scratch/Rtmp6CNj0Q’ ‘~/tmp/scratch/Rtmp7R1bIX’
‘~/tmp/scratch/Rtmp7gLzaK’ ‘~/tmp/scratch/Rtmp7tIexd’
‘~/tmp/scratch/Rtmp7yKt59’ ‘~/tmp/scratch/Rtmp88eHKn’
‘~/tmp/scratch/Rtmp8QW5jC’ ‘~/tmp/scratch/Rtmp8edxce’
‘~/tmp/scratch/Rtmp9ONYkh’ ‘~/tmp/scratch/Rtmp9tgWZJ’
‘~/tmp/scratch/RtmpAbSW6Y’ ‘~/tmp/scratch/RtmpBlfxef’
‘~/tmp/scratch/RtmpD71xJV’ ‘~/tmp/scratch/RtmpDK4c6x’
‘~/tmp/scratch/RtmpDRSWIK’ ‘~/tmp/scratch/RtmpFKKb4K’
‘~/tmp/scratch/RtmpFO0ptC’ ‘~/tmp/scratch/RtmpFcNX3L’
‘~/tmp/scratch/RtmpG1K457’ ‘~/tmp/scratch/RtmpHb90Zh’
‘~/tmp/scratch/RtmpIA6uNw’ ‘~/tmp/scratch/RtmpIBZ3iL’
‘~/tmp/scratch/RtmpIwEqHf’ ‘~/tmp/scratch/RtmpJEa0Y3’
‘~/tmp/scratch/RtmpJldwNN’ ‘~/tmp/scratch/RtmpJr1Rgo’
‘~/tmp/scratch/RtmpKP7n2O’ ‘~/tmp/scratch/RtmpKaPAnK’
‘~/tmp/scratch/RtmpKjixS0’ ‘~/tmp/scratch/RtmpKodNIt’
‘~/tmp/scratch/RtmpL2GPl0’ ‘~/tmp/scratch/RtmpL5kRwQ’
‘~/tmp/scratch/RtmpLejxQr’ ‘~/tmp/scratch/RtmpNr6xpe’
‘~/tmp/scratch/RtmpOE68g6’ ‘~/tmp/scratch/RtmpOtSQuT’
‘~/tmp/scratch/RtmpPdUM2E’ ‘~/tmp/scratch/RtmpQEy56u’
‘~/tmp/scratch/RtmpQaWZw3’ ‘~/tmp/scratch/RtmpQhBKAP’
‘~/tmp/scratch/RtmpR0WMxJ’ ‘~/tmp/scratch/RtmpRSGyzX’
‘~/tmp/scratch/RtmpSR8u4b’ ‘~/tmp/scratch/RtmpSprMfV’
‘~/tmp/scratch/RtmpT9Exis’ ‘~/tmp/scratch/RtmpTvg2Xa’
‘~/tmp/scratch/RtmpU2itF7’ ‘~/tmp/scratch/RtmpU5j1BC’
‘~/tmp/scratch/RtmpUMwSIj’ ‘~/tmp/scratch/RtmpUb3CwF’
‘~/tmp/scratch/RtmpVg4RFb’ ‘~/tmp/scratch/RtmpVntVAk’
‘~/tmp/scratch/RtmpWj2rpx’ ‘~/tmp/scratch/RtmpWvclyd’
‘~/tmp/scratch/RtmpX8tWOz’ ‘~/tmp/scratch/RtmpXEvBfG’
‘~/tmp/scratch/RtmpYFDfFJ’ ‘~/tmp/scratch/RtmpYZpKDB’
‘~/tmp/scratch/RtmpYs3cWs’ ‘~/tmp/scratch/RtmpZQiowB’
‘~/tmp/scratch/RtmpZi8ZvE’ ‘~/tmp/scratch/RtmpaEiwmH’
‘~/tmp/scratch/Rtmpb4ZaSC’ ‘~/tmp/scratch/RtmpbtbrzO’
‘~/tmp/scratch/RtmpbxdfTu’ ‘~/tmp/scratch/RtmpcDU4kE’
‘~/tmp/scratch/RtmpcRwOIc’ ‘~/tmp/scratch/RtmpcW2k3e’
‘~/tmp/scratch/Rtmpd6T7fC’ ‘~/tmp/scratch/RtmpdxssMb’
‘~/tmp/scratch/RtmpeHHplz’ ‘~/tmp/scratch/RtmpeJeb4q’
‘~/tmp/scratch/RtmpeQ40mh’ ‘~/tmp/scratch/Rtmpek0VHP’
‘~/tmp/scratch/Rtmpf5iJcw’ ‘~/tmp/scratch/RtmpflcwKU’
‘~/tmp/scratch/RtmpflrBd6’ ‘~/tmp/scratch/Rtmpft4nWo’
‘~/tmp/scratch/RtmpgFLJFr’ ‘~/tmp/scratch/RtmphyzdKH’
‘~/tmp/scratch/RtmpiIKYIg’ ‘~/tmp/scratch/RtmpiweiZa’
‘~/tmp/scratch/RtmpjIYePA’ ‘~/tmp/scratch/RtmpjrPPGx’
‘~/tmp/scratch/RtmpkHsqqR’ ‘~/tmp/scratch/RtmpkKuzAd’
‘~/tmp/scratch/RtmpkO4ymq’ ‘~/tmp/scratch/RtmpkPo0LU’
‘~/tmp/scratch/Rtmpkeq0sZ’ ‘~/tmp/scratch/RtmpkxrMQ9’
‘~/tmp/scratch/Rtmpl9AFdw’ ‘~/tmp/scratch/Rtmplh5wa5’
‘~/tmp/scratch/RtmplwlqMb’ ‘~/tmp/scratch/RtmpmM26Jn’
‘~/tmp/scratch/Rtmpmf1QV0’ ‘~/tmp/scratch/Rtmpo1bcrf’
‘~/tmp/scratch/RtmpoPx454’ ‘~/tmp/scratch/RtmpotVxbK’
‘~/tmp/scratch/RtmppRzuMn’ ‘~/tmp/scratch/Rtmppv4Wiv’
‘~/tmp/scratch/Rtmppv9966’ ‘~/tmp/scratch/RtmpqC5ABo’
‘~/tmp/scratch/RtmpqX6GvK’ ‘~/tmp/scratch/Rtmpre6D0X’
‘~/tmp/scratch/RtmpreYAMu’ ‘~/tmp/scratch/RtmprmMQOS’
‘~/tmp/scratch/RtmpsP8Euf’ ‘~/tmp/scratch/RtmpsXQuHE’
‘~/tmp/scratch/Rtmpsrxgnp’ ‘~/tmp/scratch/RtmptIQmyv’
‘~/tmp/scratch/RtmptiAsas’ ‘~/tmp/scratch/Rtmpuczskr’
‘~/tmp/scratch/Rtmpv5SFgY’ ‘~/tmp/scratch/RtmpveTy3b’
‘~/tmp/scratch/Rtmpvh5QNc’ ‘~/tmp/scratch/RtmpwPLox9’
‘~/tmp/scratch/Rtmpwl8K5z’ ‘~/tmp/scratch/RtmpxR6mhg’
‘~/tmp/scratch/RtmpxdWlwx’ ‘~/tmp/scratch/RtmpxeA1TX’
‘~/tmp/scratch/RtmpxvMuOJ’ ‘~/tmp/scratch/RtmpxxN8sq’
‘~/tmp/scratch/RtmpymxvVW’ ‘~/tmp/scratch/RtmpzA6Xwz’
‘~/tmp/scratch/RtmpzZADVc’ ‘~/tmp/scratch/RtmpzkPWdn’
‘~/tmp/scratch/xvfb-run.0H2Q4k’ ‘~/tmp/scratch/xvfb-run.0goDdb’
‘~/tmp/scratch/xvfb-run.13hG8A’ ‘~/tmp/scratch/xvfb-run.3r0rA9’
‘~/tmp/scratch/xvfb-run.4nNQIu’ ‘~/tmp/scratch/xvfb-run.5SHA8S’
‘~/tmp/scratch/xvfb-run.5xuWy4’ ‘~/tmp/scratch/xvfb-run.6s5Z3P’
‘~/tmp/scratch/xvfb-run.8pab7L’ ‘~/tmp/scratch/xvfb-run.9h9Nml’
‘~/tmp/scratch/xvfb-run.A4Rumf’ ‘~/tmp/scratch/xvfb-run.BnzZPd’
‘~/tmp/scratch/xvfb-run.DFWics’ ‘~/tmp/scratch/xvfb-run.DX31mT’
‘~/tmp/scratch/xvfb-run.Dha6Ms’ ‘~/tmp/scratch/xvfb-run.F2ankf’
‘~/tmp/scratch/xvfb-run.IE2vGc’ ‘~/tmp/scratch/xvfb-run.J6K4w1’
‘~/tmp/scratch/xvfb-run.JG7kLK’ ‘~/tmp/scratch/xvfb-run.K1tQKd’
‘~/tmp/scratch/xvfb-run.K2mTMR’ ‘~/tmp/scratch/xvfb-run.L445BW’
‘~/tmp/scratch/xvfb-run.LN3y4C’ ‘~/tmp/scratch/xvfb-run.LqFJSi’
‘~/tmp/scratch/xvfb-run.NLat3F’ ‘~/tmp/scratch/xvfb-run.NXZatG’
‘~/tmp/scratch/xvfb-run.NkUzSD’ ‘~/tmp/scratch/xvfb-run.SozX7L’
‘~/tmp/scratch/xvfb-run.TLOUjk’ ‘~/tmp/scratch/xvfb-run.UA2Qz3’
‘~/tmp/scratch/xvfb-run.UfJ5d2’ ‘~/tmp/scratch/xvfb-run.V0sPS4’
‘~/tmp/scratch/xvfb-run.V4LFJi’ ‘~/tmp/scratch/xvfb-run.V7YUQR’
‘~/tmp/scratch/xvfb-run.WcwADj’ ‘~/tmp/scratch/xvfb-run.XRlGGk’
‘~/tmp/scratch/xvfb-run.YOXfYz’ ‘~/tmp/scratch/xvfb-run.ZP1bPZ’
‘~/tmp/scratch/xvfb-run.cR8Rax’ ‘~/tmp/scratch/xvfb-run.dMyFjw’
‘~/tmp/scratch/xvfb-run.dfEWJB’ ‘~/tmp/scratch/xvfb-run.ejJtxw’
‘~/tmp/scratch/xvfb-run.fahGq3’ ‘~/tmp/scratch/xvfb-run.gShAJS’
‘~/tmp/scratch/xvfb-run.hIqNV9’ ‘~/tmp/scratch/xvfb-run.hxQckR’
‘~/tmp/scratch/xvfb-run.jhFnDW’ ‘~/tmp/scratch/xvfb-run.l0jinr’
‘~/tmp/scratch/xvfb-run.mEoZo9’ ‘~/tmp/scratch/xvfb-run.moxbmQ’
‘~/tmp/scratch/xvfb-run.r4Mf5o’ ‘~/tmp/scratch/xvfb-run.rTAFJi’
‘~/tmp/scratch/xvfb-run.sMDbXd’ ‘~/tmp/scratch/xvfb-run.sSjztK’
‘~/tmp/scratch/xvfb-run.tH3jk8’ ‘~/tmp/scratch/xvfb-run.ygWFaR’
‘~/tmp/scratch/xvfb-run.zecKlb’ ‘~/tmp/scratch/xvfb-run.zmleYu’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown
2026-08-03 06:35:11.478 R[52760:226668] XType: Using static font registry.
*** 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)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)
32: e$fun(obj, substitute(ex), parent.frame(), e$data)
33: foreach(i = 1:n.cluster) %dopar% { jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)}
34: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, n.thin = n.thin)
35: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
36: eval(expr, envir)
37: eval(expr, envir)
38: withVisible(eval(expr, envir))
39: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
40: eval(call)
41: eval(call)
42: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
43: doWithOneRestart(return(expr), restart)
44: withOneRestart(expr, restarts[[1L]])
45: withRestartList(expr, restarts[-nr])
46: doWithOneRestart(return(expr), restart)
47: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
48: withRestartList(expr, restarts)
49: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$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/RtmpNEsOWO/file983d22bfe8b5.rds")
An irrecoverable exception occurred. R is aborting now ...
*** 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)
28: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
29: FUN(X[[i]], ...)
30: lapply(seq_len(cores), inner.do)
31: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, mc.silent = silent, mc.cores = cores)
32: e$fun(obj, substitute(ex), parent.frame(), e$data)
33: foreach(i = 1:n.cluster) %dopar% { 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)}
34: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, n.thin = n.thin)
35: mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
36: eval(expr, envir)
37: eval(expr, envir)
38: withVisible(eval(expr, envir))
39: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
40: eval(call)
41: eval(call)
42: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
43: doWithOneRestart(return(expr), restart)
44: withOneRestart(expr, restarts[[1L]])
45: withRestartList(expr, restarts[-nr])
46: doWithOneRestart(return(expr), restart)
47: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
48: withRestartList(expr, restarts)
49: withRestarts(with_handlers({ for (expr in tle$exprs) { 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/RtmpNEsOWO/file983d22bfe8b5.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