makemyprior

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re-building of vignette outputs

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

_L_i_s_t _a_v_a_i_l_a_b_l_e _p_r_i_o_r_s, _l_a_t_e_n_t _m_o_d_e_l_s _a_n_d _l_i_k_e_l_i_h_o_o_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     Prints available priors, latent models and likelihoods to use with
     make_prior.

_U_s_a_g_e:

     makemyprior_models(type = c("prior", "latent", "likelihood"), select = NULL)
     
_A_r_g_u_m_e_n_t_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

_V_a_l_u_e:

     None.

_E_x_a_m_p_l_e_s:

     makemyprior_models("prior", c("pc0", "pc1"))
     makemyprior_models("latent")
     makemyprior_models("likelihood", "all")
     

--- finished re-building ‘make_prior.Rmd’

sh: line 1: 49675 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpE3mOm8/fileb74f4a75aac0' 2>&1 < '/Volumes/Temp/tmp/RtmpE3mOm8/fileb74f731d4970'
--- 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$use_intercept, family = family, latent = model_data))
 6: make_prior(formula, neonatal_data, family = "binomial", prior = list(tree = "s1 = (u, v); s2 = (s1, nu)",     w = list(s1 = list(prior = "pc0", param = 0.25), s2 = list(prior = "pc1",         param = 0.75)), V = list(s2 = list(prior = "pc", param = c(3.35,         0.05)))))
 7: eval(expr, envir)
 8: eval(expr, envir)
 9: withVisible(eval(expr, envir))
10: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({    for (expr in tle$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$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
30: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
31: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
32: process_file(text, output)
33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
35: vweave_rmarkdown(...)
36: engine$weave(file, quiet = quiet, encoding = enc)
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: 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)))})
41: 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/RtmpE3mOm8/fileb74f5b30758d.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

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Rd cross-references

Package unavailable to check Rd xrefs: ‘INLA’

package dependencies

Package suggested but not available for checking: ‘INLA’

Rd cross-references

Package unavailable to check Rd xrefs: ‘INLA’

package dependencies

Package suggested but not available for checking: ‘INLA’

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