Error(s) in re-building vignettes:
  ...
--- re-building ‘covstruct.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘covstruct.rmd’

--- re-building ‘mcmc.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘mcmc.rmd’

Segmentation Fault - core dumped
--- re-building ‘miscEx.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(y ~ x, family = beta_family(), data = dd)
 9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: withVisible(eval(expr, envir, enclos))
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
16: evaluate::evaluate(...)
17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(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))
18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options)))
19: eng_r(options)
20: block_exec(params)
21: call_block(x)
22: process_group.block(group)
23: process_group(group)
24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
25: process_file(text, output)
26: knit(input, text = text, envir = envir, quiet = quiet)
27: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv(), ...)
28: vweave(...)
29: engine$weave(file, quiet = quiet, encoding = enc)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch({    engine$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)))})
34: tools:::.buildOneVignette("miscEx.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB",     TRUE, FALSE, "miscEx", "UTF-8", "/tmp/RtmpcTaacd/working_dir/Rtmp53aaRX/file6358635f8ec.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘parallel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘parallel.Rmd’

--- re-building ‘sim.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-30 (sim.rmd) 
Error: processing vignette 'sim.rmd' failed with diagnostics:
negative log-likelihood is NaN at starting parameter values
--- failed re-building ‘sim.rmd’

Segmentation Fault - core dumped
--- re-building ‘troubleshooting.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: sparseHessianFun(env, skipFixedEffects = skipFixedEffects)
 2: he(par)
 3: newton(par = c(b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0, b = 0), fn = function (par.random, order = 0, ...) {    par[random] <- par.random    par[-random] <- par.fixed    res <- f(par, order = order, ...)    switch(order + 1, res, res[random], res[random, random])}, gr = function (x) f0(x, order = 1), he = function (par.random) {    par[random] <- par.random    par[-random] <- par.fixed    spHess(par, random = TRUE)}, env = <environment>, maxit = 1000, trace = FALSE)
 4: do.call("newton", c(list(par = eval(random.start), fn = f0, gr = function(x) f0(x,     order = 1), he = H0, env = env), inner.control))
 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)[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(do.call("newton", c(list(par = eval(random.start), fn = f0,     gr = function(x) f0(x, order = 1), he = H0, env = env), inner.control)),     silent = silent)
10: ff(x, order = 0)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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)[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))})
15: try({    if (MCcontrol$doMC) {        ff(x, order = 0)        MC(last.par, n = MCcontrol$n, seed = MCcontrol$seed,             order = 0)    }    else ff(x, order = 0)}, silent = silent)
16: obj$fn(obj$par)
17: fitTMB(TMBStruc)
18: glmmTMB(formula = taeCPUE ~ Avg.Relief + (1 | site.name/reef.name),     data = dd, family = nbinom1, ziformula = ~0, dispformula = ~1,     control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
19: eval(call, parent.frame())
20: eval(call, parent.frame())
21: update.default(mod2, control = glmmTMBControl(optimizer = optim,     optArgs = list(method = "BFGS")))
22: update(mod2, control = glmmTMBControl(optimizer = optim, optArgs = list(method = "BFGS")))
23: eval(expr, envir, enclos)
24: eval(expr, envir, enclos)
25: withVisible(eval(expr, envir, enclos))
26: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
27: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
28: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
29: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
30: evaluate::evaluate(...)
31: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$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$render, options))
32: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(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)))
33: eng_r(options)
34: block_exec(params)
35: call_block(x)
36: process_group.block(group)
37: process_group(group)
38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
39: process_file(text, output)
40: knit(input, text = text, envir = envir, quiet = quiet)
41: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv(), ...)
42: vweave(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: 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)))})
48: tools:::.buildOneVignette("troubleshooting.rmd", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB",     TRUE, FALSE, "troubleshooting", "UTF-8", "/tmp/RtmpcTaacd/working_dir/Rtmp53aaRX/file6358e403ae5.rds")
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0, cause 'memory not mapped'
--- re-building ‘glmmTMB.Rnw’ using knitr
Loading required package: stats4
--- finished re-building ‘glmmTMB.Rnw’

Segmentation Fault - core dumped
--- re-building ‘model_evaluation.Rnw’ using knitr
Loading required package: carData
lattice theme set by effectsTheme()
See ?effectsTheme for details.
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

This is DHARMa 0.4.3. For overview type '?DHARMa'. For recent changes, type news(package = 'DHARMa') Note: Syntax of plotResiduals has changed in 0.3.0, see ?plotResiduals for details
Loading required package: ggplot2
Version:  1.37.5
Date:     2020-06-17
Author:   Philip Leifeld (University of Essex)

Consider submitting praise using the praise or praise_interactive functions.
Please cite the JSS article in your publications -- see citation("texreg").

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(SiblingNegotiation ~ FoodTreatment * SexParent + (1 |     Nest) + offset(log(BroodSize)), contrasts = list(FoodTreatment = "contr.sum",     SexParent = "contr.sum"), family = nbinom1, zi = ~1, data = Owls)
 9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: withVisible(eval(expr, envir, enclos))
12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
16: evaluate::evaluate(...)
17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(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))
18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options)))
19: eng_r(options)
20: block_exec(params)
21: call_block(x)
22: process_group.block(group)
23: process_group(group)
24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
25: process_file(text, output)
26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv(), ...)
27: engine$weave(file, quiet = quiet, encoding = enc)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch({    engine$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)))})
32: tools:::.buildOneVignette("model_evaluation.Rnw", "/home/ripley/R/packages/tests32/glmmTMB.Rcheck/vign_test/glmmTMB",     TRUE, FALSE, "model_evaluation", "UTF-8", "/tmp/RtmpcTaacd/working_dir/Rtmp53aaRX/file6358752b3bf6.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
  ‘miscEx.rmd’ ‘sim.rmd’ ‘troubleshooting.rmd’ ‘model_evaluation.Rnw’

Error: Vignette re-building failed.
Execution halted