Last updated on 2026-10-16 14:51:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 4.42 | 65.59 | 70.01 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 3.01 | 50.84 | 53.85 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 46.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 51.74 | OK | |||
| r-devel-windows-x86_64 | 1.2.3 | 8.00 | 137.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 1.2.3 | 3.85 | 60.42 | 64.27 | OK | |
| r-release-linux-x86_64 | 1.2.3 | 3.28 | 60.20 | 63.48 | 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 | 1.2.2 | 7.00 | 134.00 | 141.00 | ERROR | |
| 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 | 8.00 | 132.00 | 140.00 | OK |
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in 'isoWater-Ex.R' failed
The error most likely occurred in:
> ### Name: wiDB_data
> ### Title: Obtain data from wiDB using a query
> ### Aliases: wiDB_data
>
> ### ** Examples
>
> #Download data for US precipitation in the 1990s
> vals = wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01",
+ countries = "US", types = "Precipitation")
Error in wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01", countries = "US", :
object 'd' not found
Calls: wiDB_data -> message -> paste
Execution halted
Flavor: r-release-windows-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
2026-10-16 19:29:48.346 R[68332:253586] 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, ...)
Traceback:
2: 1: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...) series = series, ...)
2:
3: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, ar(x[, i], aic = TRUE) series = series, ...)
4: 3: ar(x[, i], aic = TRUE)spectrum0.ar(x)
4:
spectrum0.ar(x) 5:
doTryCatch(return(expr), name, parentenv, handler) 5:
doTryCatch(return(expr), name, parentenv, handler) 6:
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
7:
tryCatchList(expr, classes, parentenv, handlers) 7:
8: tryCatchList(expr, classes, parentenv, handlers)tryCatch(expr, error = function(e) { call <- conditionCall(e)
if (!is.null(call)) { 8: if (identical(call[[1L]], quote(doTryCatch))) tryCatch(expr, error = function(e) { call <- sys.call(-4L) call <- conditionCall(e) dcall <- deparse(call, nlines = 1L) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L) LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) LONG <- 75L w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], sm <- strsplit(conditionMessage(e), "\n")[[1L]] type = "b") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) if (w > LONG) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], prefix <- paste0(prefix, "\n ") type = "b") } if (w > LONG) else prefix <- "Error : " prefix <- paste0(prefix, "\n ") } msg <- paste0(prefix, conditionMessage(e), "\n") else prefix <- "Error : " .Internal(seterrmessage(msg[1L])) msg <- paste0(prefix, conditionMessage(e), "\n") if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(seterrmessage(msg[1L])) cat(msg, file = outFile) if (!silent && isTRUE(getOption("show.error.messages"))) { .Internal(printDeferredWarnings()) cat(msg, file = outFile) } .Internal(printDeferredWarnings()) invisible(structure(msg, class = "try-error", condition = e)) }}) invisible(structure(msg, class = "try-error", condition = e))
}) 9: try(spectrum0.ar(x)$spec)
9: 10: try(spectrum0.ar(x)$spec)safespec0(x[[i]][, j])
10: 11: safespec0(x[[i]][, j])summary.mcmc.list(x)
11: summary.mcmc.list(x)12:
summary(x)12:
summary(x)
13: 13: mcmc2bugs(samples, model.file = model.file, program = "jags", mcmc2bugs(samples, model.file = model.file, program = "jags", DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin, checkMissing = checkMissing) n.thin = n.thin, checkMissing = checkMissing)
14: 14: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, 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) n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15: 15: eval(c.expr, envir = args, enclos = envir)eval(c.expr, envir = args, enclos = envir)
16: 16: eval(c.expr, envir = args, enclos = envir)eval(c.expr, envir = args, enclos = envir)
17: 17: doTryCatch(return(expr), name, parentenv, handler)doTryCatch(return(expr), name, parentenv, handler)
18: 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 19: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
20: 20: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
21: 21: FUN(X[[i]], ...)FUN(X[[i]], ...)
22: 22: lapply(X = S, FUN = FUN, ...)lapply(X = S, FUN = FUN, ...)
23:
doTryCatch(return(expr), name, parentenv, handler)23:
doTryCatch(return(expr), name, parentenv, handler)24:
tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])tryCatchList(expr, classes, parentenv, handlers)
25: 26: tryCatch(expr, error = function(e) {tryCatchList(expr, classes, parentenv, handlers) call <- conditionCall(e)
if (!is.null(call)) {26: if (identical(call[[1L]], quote(doTryCatch))) tryCatch(expr, error = function(e) { call <- conditionCall(e) call <- sys.call(-4L) if (!is.null(call)) { dcall <- deparse(call, nlines = 1L) if (identical(call[[1L]], quote(doTryCatch))) prefix <- paste("Error in", dcall, ": ") call <- sys.call(-4L) LONG <- 75L dcall <- deparse(call, nlines = 1L) sm <- strsplit(conditionMessage(e), "\n")[[1L]] prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") LONG <- 75L if (is.na(w)) sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") type = "b") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], if (w > LONG) prefix <- paste0(prefix, "\n ") type = "b") } if (w > LONG) else prefix <- "Error : " prefix <- paste0(prefix, "\n ") msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) } if (!silent && isTRUE(getOption("show.error.messages"))) { else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") cat(msg, file = outFile) .Internal(seterrmessage(msg[1L])) .Internal(printDeferredWarnings()) if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) invisible(structure(msg, class = "try-error", condition = e)) .Internal(printDeferredWarnings())}) }
invisible(structure(msg, class = "try-error", condition = e))27: })try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
27: 28: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
28: 29: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))FUN(X[[i]], ...)
29: FUN(X[[i]], ...)30:
lapply(seq_len(cores), inner.do)30:
lapply(seq_len(cores), inner.do)31:
mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, 31: mc.silent = silent, mc.cores = cores)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)
32: 32: e$fun(obj, substitute(ex), parent.frame(), e$data)e$fun(obj, substitute(ex), parent.frame(), e$data)
33: 33: foreach(i = 1:n.cluster) %dopar% {foreach(i = 1:n.cluster) %dopar% { jags(data = data, parameters.to.save = parameters.to.save, jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, n.chains = 1, n.iter = n.iter, model.file = model.file, n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin) n.burnin = n.burnin, n.thin = n.thin)}}
34: 34: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, jags.parallel(data = d, parameters.to.save = p, model.file = tmf, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, n.thin = n.thin) n.thin = n.thin)
35:
mixSource(obs, sources, slope, ngens = 20000, ncores = 2)35:
mixSource(obs, sources, slope, ngens = 20000, ncores = 2)36:
eval(expr, envir)36:
eval(expr, envir)37:
eval(expr, envir)37:
38: eval(expr, envir)withVisible(eval(expr, envir))
38:
39: withVisible(eval(expr, envir))
39: withCallingHandlers(code, error = function (e) withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) rlang::entrace(e), message = function (cnd) {{ watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_message$capture) { if (on_message$capture) { watcher$push(cnd) watcher$push(cnd) } } if (on_message$silence) { if (on_message$silence) { invokeRestart("muffleMessage") invokeRestart("muffleMessage") } }}, warning = function (cnd) }, warning = function (cnd) {{ if (getOption("warn") >= 2 || getOption("warn") < 0) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() return() } } watcher$capture_plot_and_output() watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) if (on_warning$capture) { } cnd <- sanitize_call(cnd) if (on_warning$silence) { watcher$push(cnd) } invokeRestart("muffleWarning") if (on_warning$silence) { invokeRestart("muffleWarning") } }}, error = function (cnd) }, error = function (cnd) {{ watcher$capture_plot_and_output() watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) cnd <- sanitize_call(cnd) watcher$push(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL) stop = invokeRestart("eval_stop"), error = NULL)})})
40: 40: eval(call)eval(call)
41: 41: eval(call)eval(call)
42: 42: with_handlers({with_handlers({ for (expr in tle$exprs) { for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) watcher$print_value(ev$value, ev$visible, envir) } } TRUE TRUE}, handlers)}, handlers)
43: 43: doWithOneRestart(return(expr), restart)doWithOneRestart(return(expr), restart)
44: 44: withOneRestart(expr, restarts[[1L]])withOneRestart(expr, restarts[[1L]])
45: withRestartList(expr, restarts[-nr])45:
withRestartList(expr, restarts[-nr])46: doWithOneRestart(return(expr), restart)
46: 47: doWithOneRestart(return(expr), restart)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
47: 48: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])withRestartList(expr, restarts)
48: 49: withRestarts(with_handlers({ for (expr in tle$exprs) {withRestartList(expr, restarts) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()49: watcher$print_value(ev$value, ev$visible, envir)withRestarts(with_handlers({ } for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) TRUE watcher$capture_plot_and_output()}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
watcher$print_value(ev$value, ev$visible, envir)50: }evaluate::evaluate(...) TRUE
51: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)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, 50: stop_on_error = if (is.numeric(options$error)) options$error else {evaluate::evaluate(...)
if (options$error && options$include) 51: 0Levaluate(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, else 2L stop_on_error = if (is.numeric(options$error)) options$error else { }, output_handler = knit_handlers(options$render, options)) if (options$error && options$include)
52: 0Lin_dir(input_dir(), expr) else 2L
}, output_handler = knit_handlers(options$render, options))53:
in_input_dir(evaluate(code, envir = env, new_device = FALSE, 52: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, in_dir(input_dir(), expr) keep_message = if (is.numeric(options$message)) TRUE else options$message,
53: stop_on_error = if (is.numeric(options$error)) options$error else {in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (options$error && options$include) keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, 0L stop_on_error = if (is.numeric(options$error)) options$error else { else 2L }, output_handler = knit_handlers(options$render, options))) if (options$error && options$include)
0L else 2L54: }, output_handler = knit_handlers(options$render, options)))eng_r(options)
55: 54: block_exec(params)eng_r(options)
56: 55: call_block(x)block_exec(params)
56: 57: call_block(x)process_group(group)
57: 58: process_group(group)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {58: if (progress && is.function(pb$interrupt)) withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(e) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 59: error <<- format(e)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }) error = function(e) {
if (progress && is.function(pb$interrupt)) 59: pb$interrupt()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), if (is_R_CMD_build() || is_R_CMD_check()) error = function(e) { error <<- format(e) if (progress && is.function(pb$interrupt)) }), list(rlang_trace_top_env = knit_global())) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 60: error <<- format(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global())) error = function(e) { if (progress && is.function(pb$interrupt))
pb$interrupt()60: if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e)xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }), list(rlang_trace_top_env = knit_global())), function(loc) { error = function(e) { setwd(wd) if (progress && is.function(pb$interrupt)) write_utf8(res, output %n% stdout()) pb$interrupt() paste0("\nQuitting from ", loc, if (!is.null(error)) if (is_R_CMD_build() || is_R_CMD_check()) paste0("\n", rule(), error, "\n", rule())) error <<- format(e)}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) }), list(rlang_trace_top_env = knit_global())), function(loc) {
setwd(wd)61: write_utf8(res, output %n% stdout())process_file(text, output) paste0("\nQuitting from ", loc, if (!is.null(error))
paste0("\n", rule(), error, "\n", rule()))62: }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
61: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)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(), ...)63:
rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 64: output_dir = getwd(), ...)vweave_rmarkdown(...)
64: 65: vweave_rmarkdown(...)engine$weave(file, quiet = quiet, encoding = enc)
65: engine$weave(file, quiet = quiet, encoding = enc)66:
doTryCatch(return(expr), name, parentenv, handler)66:
doTryCatch(return(expr), name, parentenv, handler)67:
tryCatchOne(expr, names, parentenv, handlers[[1L]])67: tryCatchOne(expr, names, parentenv, handlers[[1L]])
68: 68: tryCatchList(expr, classes, parentenv, handlers)tryCatchList(expr, classes, parentenv, handlers)
69: 69: tryCatch({tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) 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) texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", output <- find_vignette_product(name, by = "texi2pdf", engine = engine) engine = engine) } } outputs <- c(outputs, output) outputs <- c(outputs, output)}, error = function(e) {}, error = function(e) { thisOK <<- FALSE thisOK <<- FALSE fails <<- c(fails, file) fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) file, conditionMessage(e)))})})
70: 70: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3wT9fB/filec9285551330e.rds") skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/Rtmp3wT9fB/filec9285551330e.rds")
An irrecoverable exception occurred. R is aborting now ...
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