Last updated on 2026-02-11 12:51:03 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.2 | OK | ||||
| r-devel-linux-x86_64-debian-gcc | 1.2.2 | 11.67 | 117.05 | 128.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.2 | 29.00 | 259.68 | 288.68 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.2 | 31.00 | 260.89 | 291.89 | OK | |
| r-devel-macos-arm64 | 1.2.2 | 4.00 | 45.00 | 49.00 | ERROR | |
| r-devel-windows-x86_64 | 1.2.2 | 22.00 | 164.00 | 186.00 | OK | |
| r-patched-linux-x86_64 | 1.2.2 | 17.06 | 157.83 | 174.89 | OK | |
| r-release-linux-x86_64 | 1.2.2 | 17.89 | 155.38 | 173.27 | OK | |
| r-release-macos-arm64 | 1.2.2 | OK | ||||
| r-release-macos-x86_64 | 1.2.2 | 10.00 | 150.00 | 160.00 | OK | |
| r-release-windows-x86_64 | 1.2.2 | 22.00 | 163.00 | 185.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.2 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.2.2 | 11.00 | 203.00 | 214.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.2.2 | 28.00 | 210.00 | 238.00 | OK |
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘latin_square.Rmd’ using rmarkdown
--- finished re-building ‘latin_square.Rmd’
--- re-building ‘make_prior.Rmd’ using rmarkdown
makemyprior_models package:makemyprior R Documentation
_<08>L_<08>i_<08>s_<08>t _<08>a_<08>v_<08>a_<08>i_<08>l_<08>a_<08>b_<08>l_<08>e _<08>p_<08>r_<08>i_<08>o_<08>r_<08>s, _<08>l_<08>a_<08>t_<08>e_<08>n_<08>t _<08>m_<08>o_<08>d_<08>e_<08>l_<08>s _<08>a_<08>n_<08>d _<08>l_<08>i_<08>k_<08>e_<08>l_<08>i_<08>h_<08>o_<08>o_<08>d_<08>s
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Prints available priors, latent models and likelihoods to use with
make_prior.
_<08>U_<08>s_<08>a_<08>g_<08>e:
makemyprior_models(type = c("prior", "latent", "likelihood"), select = NULL)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
type: Which of priors, latent models and likelihoods to list.
Options are 'prior', 'latent' and 'likelihood'
select: Which in each group to show details about. 'NULL' gives only
list what exists (default), 'all' gives detailed information
about everything in that category. Can also ask for one or
more specific priors/latent models/likelihoods
_<08>V_<08>a_<08>l_<08>u_<08>e:
None.
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
makemyprior_models("prior", c("pc0", "pc1"))
makemyprior_models("latent")
makemyprior_models("likelihood", "all")
--- finished re-building ‘make_prior.Rmd’
sh: line 1: 13754 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmpb7KYs6/file2e9b1142798c' 2>&1 < '/Volumes/Temp/tmp/Rtmpb7KYs6/file2e9b2339df2e'
--- re-building ‘neonatal_mortality.Rmd’ using rmarkdown
*** caught segfault ***
address 0x2e, cause 'invalid permissions'
Traceback:
1: base::eigen(mat)
2: compute_rank(mat1_red)
3: reduce_matrices(list(base_mat, alt_mat))
4: calculate_pc_prior(args$node_data, args$prior_data$weights, covmats, gui = FALSE)
5: make_valid_prior_object(data = list(fixed = lapply(prior$fixed_effects, function(x) x$data), random = lapply(prior$random_effects, function(x) x$data)), args = list(node_data = node_data, prior_data = prior_data, covmats = covmats, response_name = prior$response_name, use_intercept = prior$use_intercept, family = family, latent = model_data))
6: make_prior(formula, neonatal_data, family = "binomial", prior = list(tree = "s1 = (u, v); s2 = (s1, nu)", w = list(s1 = list(prior = "pc0", param = 0.25), s2 = list(prior = "pc1", param = 0.75)), V = list(s2 = list(prior = "pc", param = c(3.35, 0.05)))))
7: eval(expr, envir)
8: eval(expr, envir)
9: withVisible(eval(expr, envir))
10: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestartList(expr, restarts[-nr])
17: doWithOneRestart(return(expr), restart)
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19: withRestartList(expr, restarts)
20: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
23: in_dir(input_dir(), expr)
24: 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$render, options)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
30: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
31: process_file(text, output)
32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
34: vweave_rmarkdown(...)
35: engine$weave(file, quiet = quiet, encoding = enc)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
40: tools:::.buildOneVignette("neonatal_mortality.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/makemyprior.Rcheck/vign_test/makemyprior", TRUE, FALSE, "neonatal_mortality", "UTF-8", "/Volumes/Temp/tmp/Rtmpb7KYs6/file2e9b1176d791.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘wheat_breeding.Rmd’ using rmarkdown
--- finished re-building ‘wheat_breeding.Rmd’
SUMMARY: processing the following file failed:
‘neonatal_mortality.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-macos-arm64
Version: 1.2.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2.2
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘INLA’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64